Last login: Mon Jun 16 08:42:27 on ttys000 (base) hibahmch@mac-mvqmt7cvdq ~ % export FREESURFER_HOME=/Applications/freesurfer (base) hibahmch@mac-mvqmt7cvdq ~ % source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /Users/hibahmch/fsl (base) hibahmch@mac-mvqmt7cvdq ~ % cd /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401 (base) hibahmch@mac-mvqmt7cvdq 20230831_os401 % cd 3d_dicom_orig (base) hibahmch@mac-mvqmt7cvdq 3d_dicom_orig % dcmunpack -src . -index-out dcm.index.dat cd /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig /Applications/freesurfer/bin/dcmunpack -src . -index-out dcm.index.dat -rwxr-xr-x 1 hibahmch wheel 36797 Jun 14 2023 /Applications/freesurfer/bin/dcmunpack --------------------------------------- --------------------------------------- Searching for matching files Tue Jun 17 08:59:19 EDT 2025 Tue Jun 17 08:59:20 EDT 2025 Found 2142 total files. Interrogating each and every one of them. Be patient. Found 7 unique series: 1 2 3 4 5 6 7 Subject reversal Date 20230831 Time 123406.920000 Institution Yale University School of Medicine 1 localizer 5 20 40 0.546875\0.546875 ROW 180 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112474083671032830 2 Sag_3D_MPRAGE_10_05 2.81 2530 7 unknown ROW 180 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112563784879533710 3 cmrr_mbep2d_diff_AP 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112593439399944136 4 cmrr_mbep2d_diff_PA 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113023774095261578 5 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113112314977671293 6 cmrr_mbep2d_boldMB4iPAT2 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113260189590879388 7 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202308311341156488326014 Tue Jun 17 09:23:35 EDT 2025 dcmunpack done (base) hibahmch@mac-mvqmt7cvdq 3d_dicom_orig % dcmunpack -src . -index-in dcm.index.dat -targ /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401 \ > -run 2 bold nii f.nii cd /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig /Applications/freesurfer/bin/dcmunpack -src . -index-in dcm.index.dat -targ /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401 -run 2 bold nii f.nii -rwxr-xr-x 1 hibahmch wheel 36797 Jun 14 2023 /Applications/freesurfer/bin/dcmunpack --------------------------------------- 1 2 bold f 0 0 --------------------------------------- Searching for matching files Tue Jun 17 09:30:44 EDT 2025 Tue Jun 17 09:30:44 EDT 2025 Found 2143 total files. Found 7 unique series: 1 2 3 4 5 6 7 Subject reversal Date 20230831 Time 123406.920000 Institution Yale University School of Medicine 1 localizer 5 20 40 0.546875\0.546875 ROW 180 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112474083671032830 2 Sag_3D_MPRAGE_10_05 2.81 2530 7 unknown ROW 180 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112563784879533710 3 cmrr_mbep2d_diff_AP 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112593439399944136 4 cmrr_mbep2d_diff_PA 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113023774095261578 5 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113112314977671293 6 cmrr_mbep2d_boldMB4iPAT2 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113260189590879388 7 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202308311341156488326014 #@# Run 2 Tue Jun 17 09:30:46 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112563784879533710 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/002/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112563784879533710 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/002/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112563784879533710... ^C (base) hibahmch@mac-mvqmt7cvdq 3d_dicom_orig % dcmunpack -src . -index-in dcm.index.dat -targ /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401 \ -run 2 bold nii f.nii \ > -run 3 bold nii f.nii \ > -run 4 bold nii f.nii \ > -run 5 bold nii f.nii \ > -run 6 bold nii f.nii \ > -run 7 bold nii f.nii cd /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig /Applications/freesurfer/bin/dcmunpack -src . -index-in dcm.index.dat -targ /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401 -run 2 bold nii f.nii -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -rwxr-xr-x 1 hibahmch wheel 36797 Jun 14 2023 /Applications/freesurfer/bin/dcmunpack --------------------------------------- 1 2 bold f 0 0 2 3 bold f 0 0 3 4 bold f 0 0 4 5 bold f 0 0 5 6 bold f 0 0 6 7 bold f 0 0 --------------------------------------- Searching for matching files Tue Jun 17 09:31:34 EDT 2025 Tue Jun 17 09:31:34 EDT 2025 Found 2143 total files. Found 7 unique series: 1 2 3 4 5 6 7 Subject reversal Date 20230831 Time 123406.920000 Institution Yale University School of Medicine 1 localizer 5 20 40 0.546875\0.546875 ROW 180 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112474083671032830 2 Sag_3D_MPRAGE_10_05 2.81 2530 7 unknown ROW 180 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112563784879533710 3 cmrr_mbep2d_diff_AP 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112593439399944136 4 cmrr_mbep2d_diff_PA 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113023774095261578 5 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113112314977671293 6 cmrr_mbep2d_boldMB4iPAT2 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113260189590879388 7 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202308311341156488326014 #@# Run 2 Tue Jun 17 09:31:36 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112563784879533710 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/002/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112563784879533710 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/002/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112563784879533710... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112563784879533710 dcmdir = /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/. Found 2141 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112564476189034066, size 131072 Convert 176 DICOM (256x256x176x1) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms TR=2530.00, TE=2.81, TI=1100.00, flip angle=7.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/002/f.nii... #@# Run 3 Tue Jun 17 09:33:03 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112593439399944136 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/003/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112593439399944136 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/003/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112593439399944136... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112593439399944136 dcmdir = /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/. Found 2141 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083112581578733135217, size 1548800 Check Siemens/Philips bvecs: expected Patient Position (0018,5100) to be 'HFS' not 'HFS' Convert 65 DICOM (110x110x64x65) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. IsDWI = 1, IsPhilipsDWI = 0 TR=2369.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.951594, -0.307357) k_ras = (-0, -0.307357, 0.951594) writing to /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/003/f.nii... Saving bvals and bvecs #@# Run 4 Tue Jun 17 09:34:30 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113023774095261578 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/004/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113023774095261578 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/004/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113023774095261578... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113023774095261578 dcmdir = /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/. Found 2141 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113011480853352165, size 1548800 Check Siemens/Philips bvecs: expected Patient Position (0018,5100) to be 'HFS' not 'HFS' Convert 65 DICOM (110x110x64x65) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. IsDWI = 1, IsPhilipsDWI = 0 TR=2369.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.951594, -0.307357) k_ras = (-0, -0.307357, 0.951594) writing to /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/004/f.nii... Saving bvals and bvecs #@# Run 5 Tue Jun 17 09:36:04 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113112314977671293 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/005/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113112314977671293 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/005/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113112314977671293... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113112314977671293 dcmdir = /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/. Found 2141 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113111313479969352, size 1452000 Convert 100 DICOM (110x110x60x100) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.951594, -0.307357) k_ras = (-0, -0.307357, 0.951594) writing to /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/005/f.nii... #@# Run 6 Tue Jun 17 09:37:30 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113260189590879388 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/006/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113260189590879388 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/006/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113260189590879388... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113260189590879388 dcmdir = /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/. Found 2141 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113174284636387838, size 1452000 Convert 1272 DICOM (110x110x60x1272) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.951594, -0.307357) k_ras = (-0, -0.307357, 0.951594) writing to /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/006/f.nii... #@# Run 7 Tue Jun 17 09:44:38 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202308311341156488326014 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/007/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202308311341156488326014 /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/007/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202308311341156488326014... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202308311341156488326014 dcmdir = /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/. Found 2141 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023083113403914889119369, size 1452000 Convert 460 DICOM (110x110x60x460) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.951594, -0.307357) k_ras = (-0, -0.307357, 0.951594) writing to /Volumes/umms-hillmera/asem_ptsd/OS401/20230831_os401/bold/007/f.nii... Started at Tue Jun 17 09:31:34 EDT 2025 Ended at Tue Jun 17 09:46:53 EDT 2025 dcmunpack-Run-Time-Min 15.32 Tue Jun 17 09:46:53 EDT 2025 dcmunpack done (base) hibahmch@mac-mvqmt7cvdq 3d_dicom_orig % cd /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193 (base) hibahmch@mac-mvqmt7cvdq 20240509_rh193 % cd 3d_dicom_orig (base) hibahmch@mac-mvqmt7cvdq 3d_dicom_orig % dcmunpack -src . -index-out dcm.index.dat cd /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig /Applications/freesurfer/bin/dcmunpack -src . -index-out dcm.index.dat -rwxr-xr-x 1 hibahmch wheel 36797 Jun 14 2023 /Applications/freesurfer/bin/dcmunpack --------------------------------------- --------------------------------------- Searching for matching files Tue Jun 17 09:48:58 EDT 2025 Tue Jun 17 09:48:59 EDT 2025 Found 2057 total files. Interrogating each and every one of them. Be patient. Found 7 unique series: 1 2 3 4 5 6 7 Subject reversal Date 20240506 Time 123408.247000 Institution Yale University School of Medicine 1 localizer 5 20 40 0.546875\0.546875 COL 180 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202405061240531905877856 2 Sag_3D_MPRAGE_10_05 2.81 2530 7 unknown ROW 180 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612494646604878978 3 cmrr_mbep2d_diff_AP 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612515184752281422 4 cmrr_mbep2d_diff_PA 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612544437596497165 5 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050613042318369415045 6 cmrr_mbep2d_boldMB4iPAT2 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202405061323351979687381 7 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202405061331522236959266 Tue Jun 17 10:09:09 EDT 2025 dcmunpack done (base) hibahmch@mac-mvqmt7cvdq 3d_dicom_orig % dcmunpack -src . -index-in dcm.index.dat -targ /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193 \ > -run 2 bold nii f.nii \ > -run 3 bold nii f.nii \ > -run 4 bold nii f.nii \ > -run 5 bold nii f.nii \ > -run 6 bold nii f.nii \ > -run 7 bold nii f.nii cd /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig /Applications/freesurfer/bin/dcmunpack -src . -index-in dcm.index.dat -targ /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193 -run 2 bold nii f.nii -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -rwxr-xr-x 1 hibahmch wheel 36797 Jun 14 2023 /Applications/freesurfer/bin/dcmunpack --------------------------------------- 1 2 bold f 0 0 2 3 bold f 0 0 3 4 bold f 0 0 4 5 bold f 0 0 5 6 bold f 0 0 6 7 bold f 0 0 --------------------------------------- Searching for matching files Tue Jun 17 10:10:57 EDT 2025 Tue Jun 17 10:10:57 EDT 2025 Found 2058 total files. Found 7 unique series: 1 2 3 4 5 6 7 Subject reversal Date 20240506 Time 123408.247000 Institution Yale University School of Medicine 1 localizer 5 20 40 0.546875\0.546875 COL 180 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202405061240531905877856 2 Sag_3D_MPRAGE_10_05 2.81 2530 7 unknown ROW 180 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612494646604878978 3 cmrr_mbep2d_diff_AP 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612515184752281422 4 cmrr_mbep2d_diff_PA 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612544437596497165 5 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050613042318369415045 6 cmrr_mbep2d_boldMB4iPAT2 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202405061323351979687381 7 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202405061331522236959266 #@# Run 2 Tue Jun 17 10:11:00 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612494646604878978 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/002/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612494646604878978 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/002/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612494646604878978... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612494646604878978 dcmdir = /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/. Found 2056 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612494990150279098, size 131072 Convert 176 DICOM (256x256x176x1) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms TR=2530.00, TE=2.81, TI=1100.00, flip angle=7.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/002/f.nii... #@# Run 3 Tue Jun 17 10:12:02 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612515184752281422 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/003/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612515184752281422 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/003/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612515184752281422... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612515184752281422 dcmdir = /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/. Found 2056 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612514458123180262, size 1548800 Check Siemens/Philips bvecs: expected Patient Position (0018,5100) to be 'HFS' not 'HFS' Convert 65 DICOM (110x110x64x65) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. IsDWI = 1, IsPhilipsDWI = 0 TR=2369.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.937889, -0.346936) k_ras = (-0, -0.346936, 0.937889) writing to /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/003/f.nii... Saving bvals and bvecs #@# Run 4 Tue Jun 17 10:13:03 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612544437596497165 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/004/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612544437596497165 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/004/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612544437596497165... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612544437596497165 dcmdir = /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/. Found 2056 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050612544437596497165, size 1548800 Check Siemens/Philips bvecs: expected Patient Position (0018,5100) to be 'HFS' not 'HFS' Convert 65 DICOM (110x110x64x65) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. IsDWI = 1, IsPhilipsDWI = 0 TR=2369.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.937889, -0.346936) k_ras = (-0, -0.346936, 0.937889) writing to /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/004/f.nii... Saving bvals and bvecs #@# Run 5 Tue Jun 17 10:14:04 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050613042318369415045 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/005/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050613042318369415045 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/005/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050613042318369415045... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050613042318369415045 dcmdir = /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/. Found 2056 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050613042043046114415, size 1452000 Convert 100 DICOM (110x110x60x100) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.937889, -0.346936) k_ras = (-0, -0.346936, 0.937889) writing to /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/005/f.nii... #@# Run 6 Tue Jun 17 10:15:08 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202405061323351979687381 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/006/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202405061323351979687381 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/006/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202405061323351979687381... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202405061323351979687381 dcmdir = /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/. Found 2056 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050613093024126532870, size 1452000 Convert 1187 DICOM (110x110x60x1187) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.937889, -0.346936) k_ras = (-0, -0.346936, 0.937889) writing to /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/006/f.nii... #@# Run 7 Tue Jun 17 10:21:15 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202405061331522236959266 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/007/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202405061331522236959266 /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/007/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202405061331522236959266... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202405061331522236959266 dcmdir = /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/. Found 2056 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024050613305596306448945, size 1452000 Convert 460 DICOM (110x110x60x460) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.937889, -0.346936) k_ras = (-0, -0.346936, 0.937889) writing to /Volumes/umms-hillmera/asem_ptsd/RH193/20240509_rh193/bold/007/f.nii... Started at Tue Jun 17 10:10:57 EDT 2025 Ended at Tue Jun 17 10:23:02 EDT 2025 dcmunpack-Run-Time-Min 12.08 Tue Jun 17 10:23:02 EDT 2025 dcmunpack done (base) hibahmch@mac-mvqmt7cvdq 3d_dicom_orig % cd /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123 (base) hibahmch@mac-mvqmt7cvdq 20230824_rm123 % cd 3d_dicom (base) hibahmch@mac-mvqmt7cvdq 3d_dicom % dcmunpack -src . -index-out dcm.index.dat cd /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom /Applications/freesurfer/bin/dcmunpack -src . -index-out dcm.index.dat -rwxr-xr-x 1 hibahmch wheel 36797 Jun 14 2023 /Applications/freesurfer/bin/dcmunpack --------------------------------------- --------------------------------------- Searching for matching files Tue Jun 17 10:29:31 EDT 2025 Tue Jun 17 10:29:31 EDT 2025 Found 1517 total files. Interrogating each and every one of them. Be patient. Found 7 unique series: 1 2 3 4 5 6 7 Subject reversal Date 20230824 Time 160128.224000 Institution Yale University School of Medicine 1 localizer 5 20 40 0.546875\0.546875 ROW 180 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417201317460602421 2 Sagt1_flashloc 2.47 200 60 0.9375\0.9375 ROW 300 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417213225289702478 3 cmrr_mbep2d_diff_AP 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417225817877505618 4 cmrr_mbep2d_diff_PA 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417272544689631058 5 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417335517573338103 6 cmrr_mbep2d_boldMB4iPAT2 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417521058317118831 7 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417592679855080990 Tue Jun 17 10:43:55 EDT 2025 dcmunpack done (base) hibahmch@mac-mvqmt7cvdq 3d_dicom % dcmunpack -src . -index-in dcm.index.dat -targ /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123 \ > -run 2 bold nii f.nii \ > -run 3 bold nii f.nii \ > -run 4 bold nii f.nii \ > -run 5 bold nii f.nii \ > -run 6 bold nii f.nii \ > -run 7 bold nii f.nii cd /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom /Applications/freesurfer/bin/dcmunpack -src . -index-in dcm.index.dat -targ /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123 -run 2 bold nii f.nii -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -rwxr-xr-x 1 hibahmch wheel 36797 Jun 14 2023 /Applications/freesurfer/bin/dcmunpack --------------------------------------- 1 2 bold f 0 0 2 3 bold f 0 0 3 4 bold f 0 0 4 5 bold f 0 0 5 6 bold f 0 0 6 7 bold f 0 0 --------------------------------------- Searching for matching files Tue Jun 17 10:45:30 EDT 2025 Tue Jun 17 10:45:30 EDT 2025 Found 1518 total files. Found 7 unique series: 1 2 3 4 5 6 7 Subject reversal Date 20230824 Time 160128.224000 Institution Yale University School of Medicine 1 localizer 5 20 40 0.546875\0.546875 ROW 180 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417201317460602421 2 Sagt1_flashloc 2.47 200 60 0.9375\0.9375 ROW 300 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417213225289702478 3 cmrr_mbep2d_diff_AP 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417225817877505618 4 cmrr_mbep2d_diff_PA 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417272544689631058 5 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417335517573338103 6 cmrr_mbep2d_boldMB4iPAT2 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417521058317118831 7 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417592679855080990 #@# Run 2 Tue Jun 17 10:45:32 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417213225289702478 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/002/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417213225289702478 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/002/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417213225289702478... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417213225289702478 dcmdir = /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/. Found 1516 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417213225881402484, size 131072 Warning: Weird CSA 'ProtocolSliceNumber' (System/Miscellaneous/ImageNumbering reversed): VALIDATE SLICETIMING AND BVECS ***USING_DCM2NIIXFSWRAPPER***: skip nii_flipZ() when sliceDir < 0 (/Users/developer/space_freesurfer/build/tulum/trunk/developer-7.4.1/packages/dcm2niix/nii_dicom_batch.cpp:saveDcm2NiiCore:6506) Convert 24 DICOM (256x256x24x1) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms TR=200.00, TE=2.47, TI=-1.00, flip angle=60.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/002/f.nii... #@# Run 3 Tue Jun 17 10:46:15 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417225817877505618 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/003/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417225817877505618 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/003/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417225817877505618... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417225817877505618 dcmdir = /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/. Found 1516 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417224525571103698, size 1548800 Check Siemens/Philips bvecs: expected Patient Position (0018,5100) to be 'HFS' not 'HFS' Convert 65 DICOM (110x110x64x65) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. IsDWI = 1, IsPhilipsDWI = 0 TR=2369.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.91496, -0.403545) k_ras = (-0, -0.403545, 0.91496) writing to /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/003/f.nii... Saving bvals and bvecs #@# Run 4 Tue Jun 17 10:46:59 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417272544689631058 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/004/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417272544689631058 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/004/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417272544689631058... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417272544689631058 dcmdir = /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/. Found 1516 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417255422535820614, size 1548800 Check Siemens/Philips bvecs: expected Patient Position (0018,5100) to be 'HFS' not 'HFS' Convert 65 DICOM (110x110x64x65) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. IsDWI = 1, IsPhilipsDWI = 0 TR=2369.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.91496, -0.403545) k_ras = (-0, -0.403545, 0.91496) writing to /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/004/f.nii... Saving bvals and bvecs #@# Run 5 Tue Jun 17 10:47:42 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417335517573338103 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/005/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417335517573338103 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/005/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417335517573338103... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417335517573338103 dcmdir = /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/. Found 1516 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417335444802737838, size 1452000 Convert 100 DICOM (110x110x60x100) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.91496, -0.403545) k_ras = (-0, -0.403545, 0.91496) writing to /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/005/f.nii... #@# Run 6 Tue Jun 17 10:48:29 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417521058317118831 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/006/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417521058317118831 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/006/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417521058317118831... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417521058317118831 dcmdir = /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/. Found 1516 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.202308241737231694756328, size 1452000 Convert 1160 DICOM (110x110x60x1160) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.91496, -0.403545) k_ras = (-0, -0.403545, 0.91496) writing to /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/006/f.nii... #@# Run 7 Tue Jun 17 10:53:55 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417592679855080990 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/007/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417592679855080990 /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/007/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417592679855080990... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417592679855080990 dcmdir = /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/. Found 1516 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2023082417581320367067453, size 1452000 Convert 99 DICOM (110x110x60x99) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.91496, -0.403545) k_ras = (-0, -0.403545, 0.91496) writing to /Volumes/umms-hillmera/asem_ptsd/RM123/20230824_rm123/bold/007/f.nii... Started at Tue Jun 17 10:45:30 EDT 2025 Ended at Tue Jun 17 10:54:47 EDT 2025 dcmunpack-Run-Time-Min 9.28 Tue Jun 17 10:54:47 EDT 2025 dcmunpack done (base) hibahmch@mac-mvqmt7cvdq 3d_dicom % cd /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690 (base) hibahmch@mac-mvqmt7cvdq 20240903_ss690 % cd 3d_dicom_orig (base) hibahmch@mac-mvqmt7cvdq 3d_dicom_orig % dcmunpack -src . -index-out dcm.index.dat cd /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig /Applications/freesurfer/bin/dcmunpack -src . -index-out dcm.index.dat -rwxr-xr-x 1 hibahmch wheel 36797 Jun 14 2023 /Applications/freesurfer/bin/dcmunpack --------------------------------------- --------------------------------------- Searching for matching files Tue Jun 17 10:55:59 EDT 2025 Tue Jun 17 10:56:00 EDT 2025 Found 2038 total files. Interrogating each and every one of them. Be patient. Found 7 unique series: 1 2 3 4 5 6 7 Subject reversal Date 20240903 Time 092738.566000 Institution Yale University School of Medicine 1 localizer 5 20 40 0.546875\0.546875 COL 180 /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309283033704176135 2 Sag_3D_MPRAGE_10_05 2.81 2530 7 unknown ROW 180 /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309372784042977297 3 cmrr_mbep2d_diff_AP 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309395858093383563 4 cmrr_mbep2d_diff_PA 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202409030942417184597401 5 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309580917194220232 6 cmrr_mbep2d_boldMB4iPAT2 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090310090854796607768 7 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090310294431241408643 Tue Jun 17 11:15:52 EDT 2025 dcmunpack done (base) hibahmch@mac-mvqmt7cvdq 3d_dicom_orig % dcmunpack -src . -index-in dcm.index.dat -targ /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690 \ > -run 2 bold nii f.nii \ > -run 3 bold nii f.nii \ > -run 4 bold nii f.nii \ > -run 5 bold nii f.nii \ > -run 6 bold nii f.nii \ > -run 7 bold nii f.nii cd /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig /Applications/freesurfer/bin/dcmunpack -src . -index-in dcm.index.dat -targ /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690 -run 2 bold nii f.nii -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -rwxr-xr-x 1 hibahmch wheel 36797 Jun 14 2023 /Applications/freesurfer/bin/dcmunpack --------------------------------------- 1 2 bold f 0 0 2 3 bold f 0 0 3 4 bold f 0 0 4 5 bold f 0 0 5 6 bold f 0 0 6 7 bold f 0 0 --------------------------------------- Searching for matching files Tue Jun 17 11:18:06 EDT 2025 Tue Jun 17 11:18:07 EDT 2025 Found 2039 total files. Found 7 unique series: 1 2 3 4 5 6 7 Subject reversal Date 20240903 Time 092738.566000 Institution Yale University School of Medicine 1 localizer 5 20 40 0.546875\0.546875 COL 180 /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309283033704176135 2 Sag_3D_MPRAGE_10_05 2.81 2530 7 unknown ROW 180 /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309372784042977297 3 cmrr_mbep2d_diff_AP 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309395858093383563 4 cmrr_mbep2d_diff_PA 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202409030942417184597401 5 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309580917194220232 6 cmrr_mbep2d_boldMB4iPAT2 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090310090854796607768 7 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090310294431241408643 #@# Run 2 Tue Jun 17 11:18:08 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309372784042977297 /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/002/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309372784042977297 /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/002/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309372784042977297... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309372784042977297 dcmdir = /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/. Found 2037 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309373038608377377, size 131072 Convert 176 DICOM (256x256x176x1) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms TR=2530.00, TE=2.81, TI=1100.00, flip angle=7.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/002/f.nii... #@# Run 3 Tue Jun 17 11:19:06 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309395858093383563 /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/003/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309395858093383563 /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/003/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309395858093383563... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309395858093383563 dcmdir = /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/. Found 2037 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202409030939161765478548, size 1548800 Check Siemens/Philips bvecs: expected Patient Position (0018,5100) to be 'HFS' not 'HFS' Convert 65 DICOM (110x110x64x65) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. IsDWI = 1, IsPhilipsDWI = 0 TR=2369.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.957319, -0.289032) k_ras = (-0, -0.289032, 0.957319) writing to /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/003/f.nii... Saving bvals and bvecs #@# Run 4 Tue Jun 17 11:20:03 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202409030942417184597401 /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/004/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202409030942417184597401 /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/004/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202409030942417184597401... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202409030942417184597401 dcmdir = /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/. Found 2037 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309422681413195465, size 1548800 Check Siemens/Philips bvecs: expected Patient Position (0018,5100) to be 'HFS' not 'HFS' Convert 65 DICOM (110x110x64x65) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. IsDWI = 1, IsPhilipsDWI = 0 TR=2369.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.957319, -0.289032) k_ras = (-0, -0.289032, 0.957319) writing to /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/004/f.nii... Saving bvals and bvecs #@# Run 5 Tue Jun 17 11:21:00 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309580917194220232 /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/005/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309580917194220232 /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/005/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309580917194220232... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309580917194220232 dcmdir = /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/. Found 2037 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090309572810744012649, size 1452000 Convert 100 DICOM (110x110x60x100) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.957319, -0.289032) k_ras = (-0, -0.289032, 0.957319) writing to /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/005/f.nii... #@# Run 6 Tue Jun 17 11:21:58 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090310090854796607768 /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/006/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090310090854796607768 /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/006/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090310090854796607768... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090310090854796607768 dcmdir = /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/. Found 2037 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090310021173040931168, size 1452000 Convert 1168 DICOM (110x110x60x1168) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.957319, -0.289032) k_ras = (-0, -0.289032, 0.957319) writing to /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/006/f.nii... #@# Run 7 Tue Jun 17 11:24:44 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090310294431241408643 /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/007/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090310294431241408643 /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/007/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090310294431241408643... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090310294431241408643 dcmdir = /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/. Found 2037 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/SS690/20240903_ss690/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024090310234835024543744, size 1452000 Convert 460 DICOM (110x110x60x460) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.957319, -0.289032) k_ras = (-0, -0.289032, 0.957319) writing to /Volumes/umms-hillmera/asem_ptsd/SS690/202040903_ss690/bold/007/f.nii... Started at Tue Jun 17 11:18:06 EDT 2025 Ended at Tue Jun 17 11:26:11 EDT 2025 dcmunpack-Run-Time-Min 8.08 Tue Jun 17 11:26:11 EDT 2025 dcmunpack done (base) hibahmch@mac-mvqmt7cvdq 3d_dicom_orig % cd /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155 (base) hibahmch@mac-mvqmt7cvdq 20240228_td155 % cd 3d_dicom (base) hibahmch@mac-mvqmt7cvdq 3d_dicom % dcmunpack -src . -index-out dcm.index.dat cd /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom /Applications/freesurfer/bin/dcmunpack -src . -index-out dcm.index.dat -rwxr-xr-x 1 hibahmch wheel 36797 Jun 14 2023 /Applications/freesurfer/bin/dcmunpack --------------------------------------- --------------------------------------- Searching for matching files Tue Jun 17 11:27:51 EDT 2025 Tue Jun 17 11:27:51 EDT 2025 Found 1763 total files. Interrogating each and every one of them. Be patient. Found 6 unique series: 1 2 3 4 5 6 Subject reversal Date 20240228 Time 125133.688000 Institution Yale University School of Medicine 1 localizer 5 20 40 0.546875\0.546875 ROW 180 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022812521180344339661 2 Sag_3D_MPRAGE_10_05 2.81 2530 7 unknown ROW 180 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.202402281301012212540459 3 cmrr_mbep2d_diff_AP 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813082517796946837 4 cmrr_mbep2d_diff_PA 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.202402281312159882769439 5 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813140030722877386 6 cmrr_mbep2d_boldMB4iPAT2 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813444826079182315 Tue Jun 17 11:43:28 EDT 2025 dcmunpack done (base) hibahmch@mac-mvqmt7cvdq 3d_dicom % dcmunpack -src . -index-in dcm.index.dat -targ /Volumes/umms-hillmera/asem_ptsd/TD155/20240228 \ > -run 2 bold nii f.nii \ > -run 3 bold nii f.nii \ > -run 4 bold nii f.nii \ > -run 5 bold nii f.nii \ > -run 6 bold nii f.nii cd /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom /Applications/freesurfer/bin/dcmunpack -src . -index-in dcm.index.dat -targ /Volumes/umms-hillmera/asem_ptsd/TD155/20240228 -run 2 bold nii f.nii -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -rwxr-xr-x 1 hibahmch wheel 36797 Jun 14 2023 /Applications/freesurfer/bin/dcmunpack --------------------------------------- 1 2 bold f 0 0 2 3 bold f 0 0 3 4 bold f 0 0 4 5 bold f 0 0 5 6 bold f 0 0 --------------------------------------- Searching for matching files Tue Jun 17 11:48:19 EDT 2025 Tue Jun 17 11:48:19 EDT 2025 Found 1764 total files. Found 6 unique series: 1 2 3 4 5 6 Subject reversal Date 20240228 Time 125133.688000 Institution Yale University School of Medicine 1 localizer 5 20 40 0.546875\0.546875 ROW 180 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022812521180344339661 2 Sag_3D_MPRAGE_10_05 2.81 2530 7 unknown ROW 180 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.202402281301012212540459 3 cmrr_mbep2d_diff_AP 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813082517796946837 4 cmrr_mbep2d_diff_PA 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.202402281312159882769439 5 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813140030722877386 6 cmrr_mbep2d_boldMB4iPAT2 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813444826079182315 #@# Run 2 Tue Jun 17 11:48:21 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.202402281301012212540459 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228/bold/002/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.202402281301012212540459 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228/bold/002/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.202402281301012212540459... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.202402281301012212540459 dcmdir = /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/. Found 1762 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813010920068440901, size 131072 Convert 176 DICOM (256x256x176x1) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms TR=2530.00, TE=2.81, TI=1100.00, flip angle=7.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to /Volumes/umms-hillmera/asem_ptsd/TD155/20240228/bold/002/f.nii... #@# Run 3 Tue Jun 17 11:49:05 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813082517796946837 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228/bold/003/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813082517796946837 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228/bold/003/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813082517796946837... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813082517796946837 dcmdir = /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/. Found 1762 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813074448779442045, size 1548800 Check Siemens/Philips bvecs: expected Patient Position (0018,5100) to be 'HFS' not 'HFS' Convert 65 DICOM (110x110x64x65) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. IsDWI = 1, IsPhilipsDWI = 0 TR=2369.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.939693, -0.34202) k_ras = (-0, -0.34202, 0.939693) writing to /Volumes/umms-hillmera/asem_ptsd/TD155/20240228/bold/003/f.nii... Saving bvals and bvecs #@# Run 4 Tue Jun 17 11:49:50 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.202402281312159882769439 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228/bold/004/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.202402281312159882769439 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228/bold/004/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.202402281312159882769439... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.202402281312159882769439 dcmdir = /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/. Found 1762 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813104244939658979, size 1548800 Check Siemens/Philips bvecs: expected Patient Position (0018,5100) to be 'HFS' not 'HFS' Convert 65 DICOM (110x110x64x65) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. IsDWI = 1, IsPhilipsDWI = 0 TR=2369.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.939693, -0.34202) k_ras = (-0, -0.34202, 0.939693) writing to /Volumes/umms-hillmera/asem_ptsd/TD155/20240228/bold/004/f.nii... Saving bvals and bvecs #@# Run 5 Tue Jun 17 11:50:42 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813140030722877386 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228/bold/005/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813140030722877386 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228/bold/005/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813140030722877386... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813140030722877386 dcmdir = /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/. Found 1762 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813135423163476164, size 1452000 Convert 100 DICOM (110x110x60x100) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.939693, -0.34202) k_ras = (-0, -0.34202, 0.939693) writing to /Volumes/umms-hillmera/asem_ptsd/TD155/20240228/bold/005/f.nii... #@# Run 6 Tue Jun 17 11:51:33 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813444826079182315 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228/bold/006/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813444826079182315 /Volumes/umms-hillmera/asem_ptsd/TD155/20240228/bold/006/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813444826079182315... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813444826079182315 dcmdir = /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/. Found 1762 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/TD155/20240228_td155/3d_dicom/./MR.1.3.12.2.1107.5.2.43.67084.2024022813274111196694649, size 1452000 Convert 1353 DICOM (110x110x60x1353) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.939693, -0.34202) k_ras = (-0, -0.34202, 0.939693) writing to /Volumes/umms-hillmera/asem_ptsd/TD155/20240228/bold/006/f.nii... Started at Tue Jun 17 11:48:19 EDT 2025 Ended at Tue Jun 17 11:58:03 EDT 2025 dcmunpack-Run-Time-Min 9.73 Tue Jun 17 11:58:03 EDT 2025 dcmunpack done (base) hibahmch@mac-mvqmt7cvdq 3d_dicom % cd /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941 (base) hibahmch@mac-mvqmt7cvdq 20240710_ti941 % cd 3d_dicom_orig (base) hibahmch@mac-mvqmt7cvdq 3d_dicom_orig % dcmunpack -src . -index-out dcm.index.dat cd /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig /Applications/freesurfer/bin/dcmunpack -src . -index-out dcm.index.dat -rwxr-xr-x 1 hibahmch wheel 36797 Jun 14 2023 /Applications/freesurfer/bin/dcmunpack --------------------------------------- --------------------------------------- Searching for matching files Tue Jun 17 12:01:32 EDT 2025 Tue Jun 17 12:01:33 EDT 2025 Found 2121 total files. Interrogating each and every one of them. Be patient. Found 7 unique series: 1 2 3 4 5 6 7 Subject reversal Date 20240710 Time 090449.484000 Institution Yale University School of Medicine 1 localizer 5 20 40 0.546875\0.546875 ROW 180 /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009052942618675605 2 Sag_3D_MPRAGE_10_05 2.81 2530 7 unknown ROW 180 /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009150251412976329 3 cmrr_mbep2d_diff_AP 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009175663964185363 4 cmrr_mbep2d_diff_PA 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009210486722303579 5 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009293796498714060 6 cmrr_mbep2d_boldMB4iPAT2 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202407100943399164828160 7 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009591639014276785 Tue Jun 17 12:24:44 EDT 2025 dcmunpack done (base) hibahmch@mac-mvqmt7cvdq 3d_dicom_orig % dcmunpack -src . -index-in dcm.index.dat -targ /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941 \ > -run 2 bold nii f.nii \ > -run 3 bold nii f.nii \ > -run 4 bold nii f.nii \ > -run 5 bold nii f.nii \ > -run 6 bold nii f.nii \ > -run 7 bold nii f.nii cd /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig /Applications/freesurfer/bin/dcmunpack -src . -index-in dcm.index.dat -targ /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941 -run 2 bold nii f.nii -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -rwxr-xr-x 1 hibahmch wheel 36797 Jun 14 2023 /Applications/freesurfer/bin/dcmunpack --------------------------------------- 1 2 bold f 0 0 2 3 bold f 0 0 3 4 bold f 0 0 4 5 bold f 0 0 5 6 bold f 0 0 6 7 bold f 0 0 --------------------------------------- Searching for matching files Tue Jun 17 12:32:44 EDT 2025 Tue Jun 17 12:32:45 EDT 2025 Found 2122 total files. Found 7 unique series: 1 2 3 4 5 6 7 Subject reversal Date 20240710 Time 090449.484000 Institution Yale University School of Medicine 1 localizer 5 20 40 0.546875\0.546875 ROW 180 /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009052942618675605 2 Sag_3D_MPRAGE_10_05 2.81 2530 7 unknown ROW 180 /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009150251412976329 3 cmrr_mbep2d_diff_AP 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009175663964185363 4 cmrr_mbep2d_diff_PA 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009210486722303579 5 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009293796498714060 6 cmrr_mbep2d_boldMB4iPAT2 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202407100943399164828160 7 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009591639014276785 #@# Run 2 Tue Jun 17 12:32:47 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009150251412976329 /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/002/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009150251412976329 /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/002/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009150251412976329... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009150251412976329 dcmdir = /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/. Found 2120 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009151144557376847, size 131072 Convert 176 DICOM (256x256x176x1) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms TR=2530.00, TE=2.81, TI=1100.00, flip angle=7.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/002/f.nii... #@# Run 3 Tue Jun 17 12:33:48 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009175663964185363 /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/003/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009175663964185363 /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/003/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009175663964185363... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009175663964185363 dcmdir = /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/. Found 2120 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009165247896578001, size 1548800 Check Siemens/Philips bvecs: expected Patient Position (0018,5100) to be 'HFS' not 'HFS' Convert 65 DICOM (110x110x64x65) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. IsDWI = 1, IsPhilipsDWI = 0 TR=2369.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.943801, -0.330514) k_ras = (-0, -0.330514, 0.943801) writing to /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/003/f.nii... Saving bvals and bvecs #@# Run 4 Tue Jun 17 12:34:47 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009210486722303579 /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/004/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009210486722303579 /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/004/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009210486722303579... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009210486722303579 dcmdir = /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/. Found 2120 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009194848042594886, size 1548800 Check Siemens/Philips bvecs: expected Patient Position (0018,5100) to be 'HFS' not 'HFS' Convert 65 DICOM (110x110x64x65) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. IsDWI = 1, IsPhilipsDWI = 0 TR=2369.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.943801, -0.330514) k_ras = (-0, -0.330514, 0.943801) writing to /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/004/f.nii... Saving bvals and bvecs #@# Run 5 Tue Jun 17 12:35:45 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009293796498714060 /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/005/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009293796498714060 /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/005/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009293796498714060... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009293796498714060 dcmdir = /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/. Found 2120 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009292778116812121, size 1452000 Convert 100 DICOM (110x110x60x100) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.943801, -0.330514) k_ras = (-0, -0.330514, 0.943801) writing to /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/005/f.nii... #@# Run 6 Tue Jun 17 12:36:43 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202407100943399164828160 /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/006/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202407100943399164828160 /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/006/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202407100943399164828160... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202407100943399164828160 dcmdir = /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/. Found 2120 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009344716060930612, size 1452000 Convert 1251 DICOM (110x110x60x1251) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.943801, -0.330514) k_ras = (-0, -0.330514, 0.943801) writing to /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/006/f.nii... #@# Run 7 Tue Jun 17 12:38:58 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009591639014276785 /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/007/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009591639014276785 /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/007/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009591639014276785... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009591639014276785 dcmdir = /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/. Found 2120 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/TI941/20240710_ti941/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2024071009573516002458266, size 1452000 Convert 460 DICOM (110x110x60x460) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.943801, -0.330514) k_ras = (-0, -0.330514, 0.943801) writing to /Volumes/umms-hillmera/asem_ptsd/TI_941/20240710_ti941/bold/007/f.nii... Started at Tue Jun 17 12:32:44 EDT 2025 Ended at Tue Jun 17 12:40:33 EDT 2025 dcmunpack-Run-Time-Min 7.82 Tue Jun 17 12:40:33 EDT 2025 dcmunpack done (base) hibahmch@mac-mvqmt7cvdq 3d_dicom_orig % cd /Volumes/umms-hillmera/asem_ptsd (base) hibahmch@mac-mvqmt7cvdq asem_ptsd % cd DW204 (base) hibahmch@mac-mvqmt7cvdq DW204 % touch subjectname.txt (base) hibahmch@mac-mvqmt7cvdq DW204 % cd 20240801_dw204 (base) hibahmch@mac-mvqmt7cvdq 20240801_dw204 % export SUBJECTS_DIR=/Volumes/umms-hillmera/asem_ptsd/DW204 (base) hibahmch@mac-mvqmt7cvdq 20240801_dw204 % preproc-sess -s 20240801_dw204 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run ERROR: cound not find session 20240801_dw204 (base) hibahmch@mac-mvqmt7cvdq 20240801_dw204 % cd /Volumes/umms-hillmera/asem_ptsd/DW204 (base) hibahmch@mac-mvqmt7cvdq DW204 % preproc-sess -s 20240801_dw204 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.20240801_dw204.log -------------------------------------------------------------- FreeSurferEnv.csh 7.4.1 hibahmch setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 /Volumes/umms-hillmera/asem_ptsd/DW204 /Applications/freesurfer/fsfast/bin/preproc-sess -s 20240801_dw204 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Tue Jun 17 12:47:34 EDT 2025 instem f mc 1 f fmcpr stc 1 fmcpr fmcpr.up sm 0 mask 1 brain 20240801_dw204 Template ----------------------------- mktemplate-sess -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -funcstem f -update Session: /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 ---------------- Tue Jun 17 12:47:35 EDT 2025 Detected input format at nii /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/f.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/template.nii.gz --frame 0 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/f.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/template.nii.gz --frame 0 reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/f.nii... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) keeping frame 0 writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/template.nii.gz... Run: 002 ---------------- Tue Jun 17 12:47:37 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/f.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/template.nii.gz --mid-frame mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/f.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/template.nii.gz --mid-frame reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/f.nii... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) keeping frame 0 writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/template.nii.gz... Run: 003 ---------------- Tue Jun 17 12:47:38 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/f.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/template.nii.gz --mid-frame mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/f.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/template.nii.gz --mid-frame reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/f.nii... INFO: This is an unsigined short. TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) keeping frame 32 writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/template.nii.gz... Run: 004 ---------------- Tue Jun 17 12:47:41 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/f.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/template.nii.gz --mid-frame mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/f.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/template.nii.gz --mid-frame reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/f.nii... INFO: This is an unsigined short. TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) keeping frame 32 writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/template.nii.gz... Run: 005 ---------------- Tue Jun 17 12:47:43 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/f.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/template.nii.gz --mid-frame mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/f.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/template.nii.gz --mid-frame reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/f.nii... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) keeping frame 50 writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/template.nii.gz... Run: 006 ---------------- Tue Jun 17 12:47:46 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/f.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/template.nii.gz --mid-frame mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/f.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/template.nii.gz --mid-frame reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/f.nii... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) keeping frame 606 writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/template.nii.gz... Run: 007 ---------------- Tue Jun 17 12:50:21 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/f.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/template.nii.gz --mid-frame mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/f.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/template.nii.gz --mid-frame reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/f.nii... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) keeping frame 230 writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/template.nii.gz... Tue Jun 17 12:50:59 EDT 2025 mktemplate-sess completed 20240801_dw204 Registration ----------------------------- register-sess -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg -------------------------------------------------------------- register-sess logfile is /Volumes/umms-hillmera/asem_ptsd/DW204/log/register-sess.20240801_dw204.log -------------------------------------------------------------- Tue Jun 17 12:50:59 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204 /Applications/freesurfer/fsfast/bin/register-sess -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 Session: /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 ---------------- Tue Jun 17 12:51:00 EDT 2025 ERROR: file 'subjectname' does not exist in /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 (base) hibahmch@mac-mvqmt7cvdq DW204 % preproc-sess -s 20240801_dw204 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.20240801_dw204.log -------------------------------------------------------------- FreeSurferEnv.csh 7.4.1 hibahmch setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 /Volumes/umms-hillmera/asem_ptsd/DW204 /Applications/freesurfer/fsfast/bin/preproc-sess -s 20240801_dw204 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Tue Jun 17 12:51:39 EDT 2025 instem f mc 1 f fmcpr stc 1 fmcpr fmcpr.up sm 0 mask 1 brain 20240801_dw204 Template ----------------------------- mktemplate-sess -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -funcstem f -update Session: /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 ---------------- Tue Jun 17 12:51:40 EDT 2025 Detected input format at nii 20240801_dw204 Update not needed Run: 002 ---------------- Tue Jun 17 12:51:40 EDT 2025 20240801_dw204 002 Update not needed Run: 003 ---------------- Tue Jun 17 12:51:40 EDT 2025 20240801_dw204 003 Update not needed Run: 004 ---------------- Tue Jun 17 12:51:41 EDT 2025 20240801_dw204 004 Update not needed Run: 005 ---------------- Tue Jun 17 12:51:41 EDT 2025 20240801_dw204 005 Update not needed Run: 006 ---------------- Tue Jun 17 12:51:41 EDT 2025 20240801_dw204 006 Update not needed Run: 007 ---------------- Tue Jun 17 12:51:41 EDT 2025 20240801_dw204 007 Update not needed Tue Jun 17 12:51:41 EDT 2025 mktemplate-sess completed 20240801_dw204 Registration ----------------------------- register-sess -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg -------------------------------------------------------------- register-sess logfile is /Volumes/umms-hillmera/asem_ptsd/DW204/log/register-sess.20240801_dw204.log -------------------------------------------------------------- Tue Jun 17 12:51:41 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204 /Applications/freesurfer/fsfast/bin/register-sess -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 Session: /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 ---------------- Tue Jun 17 12:51:42 EDT 2025 -------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 bbregister --s 20240801_dw204 --init-coreg --6 --bold --mov bold/template.nii.gz --reg bold/register.dof6.dat --lta bold/register.dof6.lta --init-reg-out bold/init.register.dof6.dat tmp bold/tmp.bbregister.89169 Log file is bold/register.dof6.log Tue Jun 17 12:51:42 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 /Applications/freesurfer/bin/bbregister --s 20240801_dw204 --init-coreg --6 --bold --mov bold/template.nii.gz --reg bold/register.dof6.dat --lta bold/register.dof6.lta --init-reg-out bold/init.register.dof6.dat FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 FREESURFER_HOME /Applications/freesurfer mri_convert bold/template.nii.gz bold/tmp.bbregister.89169/template.nii mri_convert bold/template.nii.gz bold/tmp.bbregister.89169/template.nii reading from bold/template.nii.gz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to bold/tmp.bbregister.89169/template.nii... mri_coreg --s 20240801_dw204 --mov bold/tmp.bbregister.89169/template.nii --regdat bold/tmp.bbregister.89169/reg.init.dat --reg bold/tmp.bbregister.89169/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 cmdline mri_coreg --s 20240801_dw204 --mov bold/tmp.bbregister.89169/template.nii --regdat bold/tmp.bbregister.89169/reg.init.dat --reg bold/tmp.bbregister.89169/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov bold/tmp.bbregister.89169/template.nii Reading in ref /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/brainmask.mgz error: mghRead(/Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/brainmask.mgz, -1): could not open file (base) hibahmch@mac-mvqmt7cvdq DW204 % preproc-sess -s 20240801_dw204 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.20240801_dw204.log -------------------------------------------------------------- FreeSurferEnv.csh 7.4.1 hibahmch setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 /Volumes/umms-hillmera/asem_ptsd/DW204 /Applications/freesurfer/fsfast/bin/preproc-sess -s 20240801_dw204 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Tue Jun 17 12:51:59 EDT 2025 instem f mc 1 f fmcpr stc 1 fmcpr fmcpr.up sm 0 mask 1 brain 20240801_dw204 Template ----------------------------- mktemplate-sess -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -funcstem f -update Session: /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 ---------------- Tue Jun 17 12:51:59 EDT 2025 Detected input format at nii 20240801_dw204 Update not needed Run: 002 ---------------- Tue Jun 17 12:52:00 EDT 2025 20240801_dw204 002 Update not needed Run: 003 ---------------- Tue Jun 17 12:52:00 EDT 2025 20240801_dw204 003 Update not needed Run: 004 ---------------- Tue Jun 17 12:52:00 EDT 2025 20240801_dw204 004 Update not needed Run: 005 ---------------- Tue Jun 17 12:52:00 EDT 2025 20240801_dw204 005 Update not needed Run: 006 ---------------- Tue Jun 17 12:52:00 EDT 2025 20240801_dw204 006 Update not needed Run: 007 ---------------- Tue Jun 17 12:52:00 EDT 2025 20240801_dw204 007 Update not needed Tue Jun 17 12:52:00 EDT 2025 mktemplate-sess completed 20240801_dw204 Registration ----------------------------- register-sess -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg -------------------------------------------------------------- register-sess logfile is /Volumes/umms-hillmera/asem_ptsd/DW204/log/register-sess.20240801_dw204.log -------------------------------------------------------------- Tue Jun 17 12:52:01 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204 /Applications/freesurfer/fsfast/bin/register-sess -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 Session: /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 ---------------- Tue Jun 17 12:52:01 EDT 2025 -------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 bbregister --s 20240801_dw204 --init-coreg --6 --bold --mov bold/template.nii.gz --reg bold/register.dof6.dat --lta bold/register.dof6.lta --init-reg-out bold/init.register.dof6.dat tmp bold/tmp.bbregister.89569 Log file is bold/register.dof6.log Tue Jun 17 12:52:01 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 /Applications/freesurfer/bin/bbregister --s 20240801_dw204 --init-coreg --6 --bold --mov bold/template.nii.gz --reg bold/register.dof6.dat --lta bold/register.dof6.lta --init-reg-out bold/init.register.dof6.dat FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 FREESURFER_HOME /Applications/freesurfer mri_convert bold/template.nii.gz bold/tmp.bbregister.89569/template.nii mri_convert bold/template.nii.gz bold/tmp.bbregister.89569/template.nii reading from bold/template.nii.gz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to bold/tmp.bbregister.89569/template.nii... mri_coreg --s 20240801_dw204 --mov bold/tmp.bbregister.89569/template.nii --regdat bold/tmp.bbregister.89569/reg.init.dat --reg bold/tmp.bbregister.89569/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 cmdline mri_coreg --s 20240801_dw204 --mov bold/tmp.bbregister.89569/template.nii --regdat bold/tmp.bbregister.89569/reg.init.dat --reg bold/tmp.bbregister.89569/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov bold/tmp.bbregister.89569/template.nii Reading in ref /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/brainmask.mgz Reading in and applying refmask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz Setting cras translation parameters to align volume centers Init matrix params -1.0000 0.0000 -1.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 1.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 1.00000; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt -1.0000 0.0000 -1.0000 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 1199.0000 mov gstd 1.8914 1.8914 1.8914 Smoothing mov refsat = 116.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0315854939 nhits = 179166 out of 16777216, Percent Overlap: 68.3 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -1.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 -1.00000; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.00000 0.00000 -1.00000 255.00000; 0.00000 1.00000 0.00000 0.00000; -1.00000 0.00000 0.00000 215.00000; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -1.00000 0.00000 -1.00000 0.00000 0.00000 0.00000 -1.0287818 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: -1.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0315854549 #@# 4 188 -1.00000 0.00000 -1.00000 0.00000 0.00000 0.00000 -1.0315855 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.031585 #@# 4 190 0.00000 0.00000 -1.00000 0.00000 0.00000 0.00000 -1.0326102 #@# 4 195 -0.03725 0.00000 -1.00000 0.00000 0.00000 0.00000 -1.0326129 #@# 4 196 -0.04725 0.00000 -1.00000 0.00000 0.00000 0.00000 -1.0326132 #@# 4 204 -0.04725 -0.04875 -1.00000 0.00000 0.00000 0.00000 -1.0326172 #@# 4 205 -0.04725 -0.09278 -1.00000 0.00000 0.00000 0.00000 -1.0326179 #@# 4 206 -0.04725 -0.08204 -1.00000 0.00000 0.00000 0.00000 -1.0326182 #@# 4 214 -0.04725 -0.07204 -0.61803 0.00000 0.00000 0.00000 -1.0327752 #@# 4 226 -0.04725 -0.07204 -0.59803 -0.05116 0.00000 0.00000 -1.0327843 #@# 4 228 -0.04725 -0.07204 -0.59803 -0.11762 0.00000 0.00000 -1.0327885 #@# 4 229 -0.04725 -0.07204 -0.59803 -0.10762 0.00000 0.00000 -1.0327886 #@# 4 246 -0.04725 -0.07204 -0.59803 -0.10762 -0.01239 -0.01000 -1.0327888 powell nthiter 1: fret = -1.032789 #@# 4 255 -0.03374 -0.07204 -0.59803 -0.10762 -0.01239 -0.01000 -1.0327892 #@# 4 263 -0.03374 -0.00521 -0.59803 -0.10762 -0.01239 -0.01000 -1.0327957 #@# 4 273 -0.03374 -0.00521 -0.64797 -0.10762 -0.01239 -0.01000 -1.0327982 #@# 4 282 -0.03374 -0.00521 -0.63797 -0.11762 -0.01239 -0.01000 -1.0327984 #@# 4 300 -0.03374 -0.00521 -0.63797 -0.13427 -0.01239 -0.02000 -1.0327985 Powell done niters total = 1 OptTimeSec 5.1 sec OptTimeMin 0.08 min nEvals 301 Final optimized parameters -0.03373676 -0.00521132 -0.63796526 -0.13427094 -0.01238912 -0.02000000 Final matrix parameters -0.0337 -0.0052 -0.6380 -0.1343 -0.0124 -0.0300 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.032798579752070 --------------------------------- Final RefRAS-to-MovRAS 1.00000 -0.00035 -0.00022 -0.03374; 0.00035 1.00000 -0.00234 -0.00521; 0.00022 0.00234 1.00000 -0.63797; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.00035 -0.00234 -1.00000 255.26440; 0.00022 1.00000 -0.00234 -0.16085; -1.00000 0.00022 -0.00035 215.97224; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters -0.0337 -0.0052 -0.6380 -0.1343 -0.0124 -0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters -0.0337 -0.0052 -0.6380 -0.1343 -0.0124 -0.0200 nhits = 178404 out of 16777216, Percent Overlap: 68.1 mri_coreg RunTimeSec 36.1 sec To check run: tkregisterfv --mov bold/tmp.bbregister.89569/template.nii --targ /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/brainmask.mgz --reg bold/tmp.bbregister.89569/mri_coreg.lta --s 20240801_dw204 --surfs mri_coreg done mri_segreg --mov bold/tmp.bbregister.89569/template.nii --init-reg bold/tmp.bbregister.89569/reg.init.dat --out-reg bold/tmp.bbregister.89569/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 mri_segreg --mov bold/tmp.bbregister.89569/template.nii --init-reg bold/tmp.bbregister.89569/reg.init.dat --out-reg bold/tmp.bbregister.89569/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/tmp.bbregister.89569/template.nii regfile bold/tmp.bbregister.89569/reg.init.dat subject 20240801_dw204 dof 6 outregfile bold/tmp.bbregister.89569/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750217188 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.00035 1.00000 -0.00234 0.99059; 1.00000 -0.00035 -0.00022 -0.04475; 0.00022 0.00234 1.00000 0.43340; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.031526 1 -25.0 -25.0 25.0 1.047528 2 -25.0 25.0 -25.0 0.993458 3 -25.0 25.0 25.0 1.017234 4 25.0 -25.0 -25.0 1.053308 5 25.0 -25.0 25.0 1.037679 6 25.0 25.0 -25.0 1.056287 7 25.0 25.0 25.0 0.993897 REL: 8 1.937984 8.230918 1.028865 rel = 1.88361 Initial costs ---------------- Number of surface hits 2538 WM Intensity 392.4088 +/- 79.1836 Ctx Intensity 260.6141 +/- 54.4622 Pct Contrast -40.0498 +/- 17.8701 Cost 1.9380 RelCost 1.8836 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0542 1.0542 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0540 1.0540 0.0 9 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 -4.0000 1.0527 1.0527 0.0 12 -4.0000 -4.0000 -4.0000 0.0000 0.0000 -4.0000 1.0425 1.0425 0.0 13 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.0000 1.0265 1.0265 0.0 94 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.0000 1.0179 1.0179 0.0 185 -4.0000 4.0000 -4.0000 4.0000 0.0000 4.0000 1.0157 1.0157 0.0 Brute Force -------------------------- Min cost was 1.015726 Number of iterations 729 Search time 1.260250 sec Parameters at best (transmm, rotdeg) -4.000 4.000 -4.000 4.000 0.000 4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -4 1 4 2 -4 3 4 4 0 5 4 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 1.015726 5 -4.618 4.000 -4.000 4.000 0.000 4.000 1.0108893622 8 -4.764 4.000 -4.000 4.000 0.000 4.000 1.0064498007 12 -4.765 4.000 -4.000 4.000 0.000 4.000 1.0064428948 13 -4.769 4.000 -4.000 4.000 0.000 4.000 1.0064281301 15 -4.770 4.000 -4.000 4.000 0.000 4.000 1.0064277553 25 -4.770 4.052 -4.000 4.000 0.000 4.000 1.0060640775 27 -4.770 4.049 -4.000 4.000 0.000 4.000 1.0060591880 49 -4.770 4.049 -4.000 4.055 0.000 4.000 1.0044269396 51 -4.770 4.049 -4.000 4.056 0.000 4.000 1.0044235846 52 -4.770 4.049 -4.000 4.057 0.000 4.000 1.0044223544 61 -4.770 4.049 -4.000 4.057 0.007 4.000 1.0042814651 64 -4.770 4.049 -4.000 4.057 0.020 4.000 1.0042003072 65 -4.770 4.049 -4.000 4.057 0.019 4.000 1.0041980141 66 -4.770 4.049 -4.000 4.057 0.018 4.000 1.0041961108 68 -4.770 4.049 -4.000 4.057 0.017 4.000 1.0041949962 79 -4.770 4.049 -4.000 4.057 0.017 4.017 1.0040195954 80 -4.770 4.049 -4.000 4.057 0.017 4.013 1.0040017249 powell nthiter 1: fret = 1.004002 94 -4.774 4.049 -4.000 4.057 0.017 4.013 1.0039991326 95 -4.773 4.049 -4.000 4.057 0.017 4.013 1.0039986513 96 -4.772 4.049 -4.000 4.057 0.017 4.013 1.0039982514 106 -4.772 4.056 -4.000 4.057 0.017 4.013 1.0039661195 108 -4.772 4.055 -4.000 4.057 0.017 4.013 1.0039639892 119 -4.772 4.055 -3.961 4.057 0.017 4.013 1.0034739404 122 -4.772 4.055 -3.962 4.057 0.017 4.013 1.0034739315 131 -4.772 4.055 -3.962 4.099 0.017 4.013 1.0031020612 135 -4.772 4.055 -3.962 4.102 0.017 4.013 1.0030887978 137 -4.772 4.055 -3.962 4.103 0.017 4.013 1.0030886738 145 -4.772 4.055 -3.962 4.103 0.000 4.013 1.0030606529 147 -4.772 4.055 -3.962 4.103 0.007 4.013 1.0030303853 148 -4.772 4.055 -3.962 4.103 0.008 4.013 1.0030299515 powell nthiter 2: fret = 1.003030 172 -4.758 4.055 -3.962 4.103 0.008 4.013 1.0030049103 174 -4.764 4.055 -3.962 4.103 0.008 4.013 1.0029631359 186 -4.764 4.056 -3.962 4.103 0.008 4.013 1.0029580979 187 -4.764 4.058 -3.962 4.103 0.008 4.013 1.0029519914 199 -4.764 4.058 -3.936 4.103 0.008 4.013 1.0025955556 200 -4.764 4.058 -3.935 4.103 0.008 4.013 1.0025893059 202 -4.764 4.058 -3.931 4.103 0.008 4.013 1.0025772365 203 -4.764 4.058 -3.930 4.103 0.008 4.013 1.0025761674 204 -4.764 4.058 -3.929 4.103 0.008 4.013 1.0025758890 214 -4.764 4.058 -3.929 4.107 0.008 4.013 1.0024975362 215 -4.764 4.058 -3.929 4.121 0.008 4.013 1.0023449705 220 -4.764 4.058 -3.929 4.123 0.008 4.013 1.0023378472 221 -4.764 4.058 -3.929 4.124 0.008 4.013 1.0023376089 229 -4.764 4.058 -3.929 4.124 -0.009 4.013 1.0021966702 233 -4.764 4.058 -3.929 4.124 -0.010 4.013 1.0021951609 234 -4.764 4.058 -3.929 4.124 -0.011 4.013 1.0021949547 244 -4.764 4.058 -3.929 4.124 -0.011 4.010 1.0021729741 246 -4.764 4.058 -3.929 4.124 -0.011 4.008 1.0021644227 247 -4.764 4.058 -3.929 4.124 -0.011 4.007 1.0021638596 powell nthiter 3: fret = 1.002164 263 -4.763 4.058 -3.929 4.124 -0.011 4.007 1.0021607316 276 -4.763 4.056 -3.929 4.124 -0.011 4.007 1.0021552825 287 -4.763 4.056 -3.928 4.124 -0.011 4.007 1.0021384585 288 -4.763 4.056 -3.919 4.124 -0.011 4.007 1.0020907308 290 -4.763 4.056 -3.921 4.124 -0.011 4.007 1.0020904075 292 -4.763 4.056 -3.920 4.124 -0.011 4.007 1.0020894278 302 -4.763 4.056 -3.920 4.119 -0.011 4.007 1.0020872253 303 -4.763 4.056 -3.920 4.121 -0.011 4.007 1.0020834128 314 -4.763 4.056 -3.920 4.121 -0.015 4.007 1.0020773493 315 -4.763 4.056 -3.920 4.121 -0.014 4.007 1.0020771304 329 -4.763 4.056 -3.920 4.121 -0.014 4.005 1.0020726010 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.017596 1 -25.0 -25.0 25.0 1.036536 2 -25.0 25.0 -25.0 1.015611 3 -25.0 25.0 25.0 1.034368 4 25.0 -25.0 -25.0 1.020799 5 25.0 -25.0 25.0 1.051545 6 25.0 25.0 -25.0 1.055021 7 25.0 25.0 25.0 1.022751 REL: 8 1.002073 8.254226 1.031778 rel = 0.971209 Number of iterations 3 Min cost was 1.002073 Number of FunctionCalls 331 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.572521 sec Parameters at optimum (transmm) -4.76321 4.05565 -3.92043 Parameters at optimum (rotdeg) 4.12082 -0.01435 4.00480 Final costs ---------------- Number of surface hits 2538 WM Intensity 302.9852 +/- 112.1439 Ctx Intensity 301.7366 +/- 116.3660 Pct Contrast -1.4851 +/- 41.3728 Cost 1.0021 RelCost 1.8836 Reg at min cost was -0.06933 0.99759 0.00245 -3.76985; 0.99499 0.06932 -0.07208 4.04924; 0.07208 0.00256 0.99740 -3.49112; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/tmp.bbregister.89569/bbr.pass1.dat, type = 14 Original Reg 0.00035 1.00000 -0.00234 0.99059; 1.00000 -0.00035 -0.00022 -0.04475; 0.00022 0.00234 1.00000 0.43340; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.06968 0.00241 -0.00479 4.76044; 0.00501 -0.06967 0.07186 -4.09398; -0.07186 -0.00022 0.00260 3.92452; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 7.490767 Computing change in rh position Surface-RMS-Diff-mm 7.614866 1.148211 11.105092 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov bold/tmp.bbregister.89569/template.nii --init-reg bold/tmp.bbregister.89569/bbr.pass1.dat --out-reg bold/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/tmp.bbregister.89569/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 mri_segreg --mov bold/tmp.bbregister.89569/template.nii --init-reg bold/tmp.bbregister.89569/bbr.pass1.dat --out-reg bold/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/tmp.bbregister.89569/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/tmp.bbregister.89569/template.nii regfile bold/tmp.bbregister.89569/bbr.pass1.dat subject 20240801_dw204 dof 6 outregfile bold/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750741471 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.06933 0.99759 0.00245 -3.76985; 0.99499 0.06932 -0.07208 4.04924; 0.07208 0.00256 0.99740 -3.49112; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.027868 1 -25.0 -25.0 25.0 1.043856 2 -25.0 25.0 -25.0 1.031360 3 -25.0 25.0 25.0 1.034708 4 25.0 -25.0 -25.0 1.032571 5 25.0 -25.0 25.0 1.015032 6 25.0 25.0 -25.0 1.039001 7 25.0 25.0 25.0 1.018414 REL: 8 1.049314 8.242809 1.030351 rel = 1.0184 Initial costs ---------------- Number of surface hits 253432 WM Intensity 307.3857 +/- 111.0625 Ctx Intensity 305.8452 +/- 115.8493 Pct Contrast -1.7254 +/- 40.9277 Cost 1.0493 RelCost 1.0184 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 1.0152 1.0152 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 1.0134 1.0134 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 1.0129 1.0129 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 1.0113 1.0113 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 1.0096 1.0096 0.0 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 1.0095 1.0095 0.0 40 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0000 1.0083 1.0083 0.0 52 -0.1000 -0.1000 0.0000 0.1000 0.1000 0.0000 1.0079 1.0079 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0063 1.0063 0.0 130 -0.1000 0.0000 0.0000 0.1000 0.0000 0.0000 1.0056 1.0056 0.0 215 -0.1000 0.1000 0.0000 0.1000 0.1000 0.1000 1.0035 1.0035 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0021 1.0021 0.0 Brute Force -------------------------- Min cost was 1.002073 Number of iterations 729 Search time 0.675606 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 1.049314 2 1.000 0.000 0.000 0.000 0.000 0.000 1.0425582378 5 1.618 0.000 0.000 0.000 0.000 0.000 1.0405346135 8 1.761 0.000 0.000 0.000 0.000 0.000 1.0403860276 10 1.703 0.000 0.000 0.000 0.000 0.000 1.0403128750 12 1.702 0.000 0.000 0.000 0.000 0.000 1.0403128121 18 1.701 0.000 0.000 0.000 0.000 0.000 1.0403127689 20 1.701 1.000 0.000 0.000 0.000 0.000 1.0394701013 21 1.701 2.618 0.000 0.000 0.000 0.000 1.0334044390 22 1.701 5.236 0.000 0.000 0.000 0.000 1.0305819580 23 1.701 4.782 0.000 0.000 0.000 0.000 1.0299212312 30 1.701 4.789 0.000 0.000 0.000 0.000 1.0298990207 31 1.701 4.808 0.000 0.000 0.000 0.000 1.0298602021 32 1.701 4.823 0.000 0.000 0.000 0.000 1.0298503477 33 1.701 4.822 0.000 0.000 0.000 0.000 1.0298496035 35 1.701 4.821 0.000 0.000 0.000 0.000 1.0298493158 38 1.701 4.821 1.000 0.000 0.000 0.000 1.0184644820 39 1.701 4.821 2.618 0.000 0.000 0.000 1.0175220701 40 1.701 4.821 1.880 0.000 0.000 0.000 1.0145558399 42 1.701 4.821 1.544 0.000 0.000 0.000 1.0143296688 44 1.701 4.821 1.679 0.000 0.000 0.000 1.0143169919 48 1.701 4.821 1.658 0.000 0.000 0.000 1.0142962736 50 1.701 4.821 1.662 0.000 0.000 0.000 1.0142955787 52 1.701 4.821 1.660 0.000 0.000 0.000 1.0142955586 56 1.701 4.821 1.660 -1.618 0.000 0.000 1.0076658029 60 1.701 4.821 1.660 -2.618 0.000 0.000 1.0059208093 65 1.701 4.821 1.660 -2.647 0.000 0.000 1.0058017903 66 1.701 4.821 1.660 -2.726 0.000 0.000 1.0057984528 67 1.701 4.821 1.660 -2.687 0.000 0.000 1.0057678330 68 1.701 4.821 1.660 -2.688 0.000 0.000 1.0057674254 69 1.701 4.821 1.660 -2.693 0.000 0.000 1.0057649648 70 1.701 4.821 1.660 -2.706 0.000 0.000 1.0057589965 72 1.701 4.821 1.660 -2.703 0.000 0.000 1.0057584633 73 1.701 4.821 1.660 -2.704 0.000 0.000 1.0057583062 82 1.701 4.821 1.660 -2.704 -0.052 0.000 1.0056586517 84 1.701 4.821 1.660 -2.704 -0.049 0.000 1.0056573977 86 1.701 4.821 1.660 -2.704 -0.048 0.000 1.0056573439 92 1.701 4.821 1.660 -2.704 -0.048 -0.618 1.0055623767 94 1.701 4.821 1.660 -2.704 -0.048 -0.323 1.0050363090 95 1.701 4.821 1.660 -2.704 -0.048 -0.322 1.0050307356 96 1.701 4.821 1.660 -2.704 -0.048 -0.199 1.0047273305 99 1.701 4.821 1.660 -2.704 -0.048 -0.168 1.0047097698 103 1.701 4.821 1.660 -2.704 -0.048 -0.166 1.0047083269 powell nthiter 1: fret = 1.004708 108 2.701 4.821 1.660 -2.704 -0.048 -0.166 1.0027624557 111 3.319 4.821 1.660 -2.704 -0.048 -0.166 1.0026303264 113 3.026 4.821 1.660 -2.704 -0.048 -0.166 1.0023752238 114 3.042 4.821 1.660 -2.704 -0.048 -0.166 1.0023476357 115 3.126 4.821 1.660 -2.704 -0.048 -0.166 1.0022096652 117 3.158 4.821 1.660 -2.704 -0.048 -0.166 1.0021338127 118 3.162 4.821 1.660 -2.704 -0.048 -0.166 1.0021292068 120 3.168 4.821 1.660 -2.704 -0.048 -0.166 1.0021246784 125 3.168 5.821 1.660 -2.704 -0.048 -0.166 1.0008376491 129 3.168 5.439 1.660 -2.704 -0.048 -0.166 0.9997791133 132 3.168 5.412 1.660 -2.704 -0.048 -0.166 0.9997473296 138 3.168 5.415 1.660 -2.704 -0.048 -0.166 0.9997450836 142 3.168 5.415 2.660 -2.704 -0.048 -0.166 0.9975964869 146 3.168 5.415 2.278 -2.704 -0.048 -0.166 0.9963778716 149 3.168 5.415 2.203 -2.704 -0.048 -0.166 0.9963215111 151 3.168 5.415 2.233 -2.704 -0.048 -0.166 0.9962248670 154 3.168 5.415 2.234 -2.704 -0.048 -0.166 0.9962244950 162 3.168 5.415 2.235 -2.829 -0.048 -0.166 0.9961014322 163 3.168 5.415 2.235 -2.861 -0.048 -0.166 0.9961006639 168 3.168 5.415 2.235 -2.871 -0.048 -0.166 0.9960954605 176 3.168 5.415 2.235 -2.870 -0.666 -0.166 0.9938030914 178 3.168 5.415 2.235 -2.870 -0.516 -0.166 0.9937327659 179 3.168 5.415 2.235 -2.870 -0.565 -0.166 0.9937080203 180 3.168 5.415 2.235 -2.870 -0.567 -0.166 0.9937030636 182 3.168 5.415 2.235 -2.870 -0.582 -0.166 0.9936984288 183 3.168 5.415 2.235 -2.870 -0.575 -0.166 0.9936955853 186 3.168 5.415 2.235 -2.870 -0.574 -0.166 0.9936954171 187 3.168 5.415 2.235 -2.870 -0.573 -0.166 0.9936953971 192 3.168 5.415 2.235 -2.870 -0.573 -0.784 0.9920963676 198 3.168 5.415 2.235 -2.870 -0.573 -0.790 0.9920934094 powell nthiter 2: fret = 0.992093 210 3.550 5.415 2.235 -2.870 -0.573 -0.791 0.9916388562 211 3.536 5.415 2.235 -2.870 -0.573 -0.791 0.9916043419 213 3.491 5.415 2.235 -2.870 -0.573 -0.791 0.9914728254 215 3.484 5.415 2.235 -2.870 -0.573 -0.791 0.9914662401 216 3.481 5.415 2.235 -2.870 -0.573 -0.791 0.9914652394 217 3.479 5.415 2.235 -2.870 -0.573 -0.791 0.9914648069 224 3.479 4.797 2.235 -2.870 -0.573 -0.791 0.9899755524 226 3.479 4.987 2.235 -2.870 -0.573 -0.791 0.9892000267 228 3.479 4.944 2.235 -2.870 -0.573 -0.791 0.9891015070 229 3.479 4.927 2.235 -2.870 -0.573 -0.791 0.9890892444 231 3.479 4.933 2.235 -2.870 -0.573 -0.791 0.9890862342 232 3.479 4.932 2.235 -2.870 -0.573 -0.791 0.9890860383 235 3.479 4.932 3.235 -2.870 -0.573 -0.791 0.9876035172 239 3.479 4.932 2.853 -2.870 -0.573 -0.791 0.9874969698 240 3.479 4.932 3.028 -2.870 -0.573 -0.791 0.9874059176 242 3.479 4.932 3.107 -2.870 -0.573 -0.791 0.9873263860 243 3.479 4.932 3.095 -2.870 -0.573 -0.791 0.9873093894 244 3.479 4.932 3.082 -2.870 -0.573 -0.791 0.9873023751 246 3.479 4.932 3.086 -2.870 -0.573 -0.791 0.9873007114 248 3.479 4.932 3.085 -2.870 -0.573 -0.791 0.9873005754 263 3.479 4.932 3.085 -2.867 -0.573 -0.791 0.9872997725 272 3.479 4.932 3.085 -2.865 -1.191 -0.791 0.9825817425 275 3.479 4.932 3.085 -2.865 -1.211 -0.791 0.9825752935 276 3.479 4.932 3.085 -2.865 -1.222 -0.791 0.9825532439 277 3.479 4.932 3.085 -2.865 -1.248 -0.791 0.9824697604 278 3.479 4.932 3.085 -2.865 -1.264 -0.791 0.9824625159 279 3.479 4.932 3.085 -2.865 -1.259 -0.791 0.9824548937 282 3.479 4.932 3.085 -2.865 -1.258 -0.791 0.9824547453 287 3.479 4.932 3.085 -2.865 -1.258 -1.409 0.9822324794 289 3.479 4.932 3.085 -2.865 -1.258 -1.197 0.9811880963 290 3.479 4.932 3.085 -2.865 -1.258 -1.114 0.9809479105 293 3.479 4.932 3.085 -2.865 -1.258 -1.126 0.9809168387 296 3.479 4.932 3.085 -2.865 -1.258 -1.129 0.9809125557 297 3.479 4.932 3.085 -2.865 -1.258 -1.131 0.9809122830 299 3.790 4.448 3.935 -2.860 -1.943 -1.470 0.9778431833 305 3.671 4.633 3.611 -2.862 -1.681 -1.340 0.9776454533 306 3.723 4.553 3.752 -2.861 -1.795 -1.397 0.9771949016 307 3.725 4.549 3.758 -2.861 -1.800 -1.399 0.9771755812 309 3.730 4.541 3.773 -2.861 -1.812 -1.405 0.9771647912 310 3.729 4.543 3.769 -2.861 -1.809 -1.404 0.9771625621 powell nthiter 3: fret = 0.977163 322 3.732 4.543 3.769 -2.861 -1.809 -1.404 0.9771611809 324 3.734 4.543 3.769 -2.861 -1.809 -1.404 0.9771611215 332 3.734 4.659 3.769 -2.861 -1.809 -1.404 0.9765374912 333 3.734 4.693 3.769 -2.861 -1.809 -1.404 0.9765203613 336 3.734 4.727 3.769 -2.861 -1.809 -1.404 0.9764378216 337 3.734 4.748 3.769 -2.861 -1.809 -1.404 0.9764374867 338 3.734 4.738 3.769 -2.861 -1.809 -1.404 0.9764338839 339 3.734 4.739 3.769 -2.861 -1.809 -1.404 0.9764329382 340 3.734 4.742 3.769 -2.861 -1.809 -1.404 0.9764307363 343 3.734 4.743 3.769 -2.861 -1.809 -1.404 0.9764304543 350 3.734 4.743 3.686 -2.861 -1.809 -1.404 0.9764145041 351 3.734 4.743 3.719 -2.861 -1.809 -1.404 0.9763850894 352 3.734 4.743 3.723 -2.861 -1.809 -1.404 0.9763847711 354 3.734 4.743 3.741 -2.861 -1.809 -1.404 0.9763756603 358 3.734 4.743 3.742 -2.861 -1.809 -1.404 0.9763754524 359 3.734 4.743 3.743 -2.861 -1.809 -1.404 0.9763754105 365 3.734 4.743 3.743 -2.479 -1.809 -1.404 0.9761646049 373 3.734 4.743 3.743 -2.489 -1.809 -1.404 0.9761553135 375 3.734 4.743 3.743 -2.488 -1.809 -1.404 0.9761547904 377 3.734 4.743 3.743 -2.487 -1.809 -1.404 0.9761546885 383 3.734 4.743 3.743 -2.487 -1.809 -2.022 0.9754989718 384 3.734 4.743 3.743 -2.487 -1.809 -2.404 0.9753514382 389 3.734 4.743 3.743 -2.487 -1.809 -2.390 0.9753154019 392 3.734 4.743 3.743 -2.487 -1.809 -2.391 0.9753153704 400 3.754 4.711 3.798 -2.486 -1.854 -2.413 0.9753039505 401 3.746 4.723 3.777 -2.486 -1.836 -2.405 0.9752356808 402 3.744 4.726 3.772 -2.486 -1.832 -2.402 0.9752338443 406 3.744 4.727 3.771 -2.486 -1.831 -2.402 0.9752337585 powell nthiter 4: fret = 0.975234 414 4.126 4.727 3.771 -2.486 -1.831 -2.402 0.9750910544 416 4.362 4.727 3.771 -2.486 -1.831 -2.402 0.9749830352 418 4.272 4.727 3.771 -2.486 -1.831 -2.402 0.9749700239 419 4.300 4.727 3.771 -2.486 -1.831 -2.402 0.9749526266 421 4.296 4.727 3.771 -2.486 -1.831 -2.402 0.9749501512 422 4.287 4.727 3.771 -2.486 -1.831 -2.402 0.9749467506 424 4.290 4.727 3.771 -2.486 -1.831 -2.402 0.9749463999 426 4.289 4.727 3.771 -2.486 -1.831 -2.402 0.9749463711 433 4.289 4.592 3.771 -2.486 -1.831 -2.402 0.9747513421 434 4.289 4.581 3.771 -2.486 -1.831 -2.402 0.9747300956 436 4.289 4.512 3.771 -2.486 -1.831 -2.402 0.9746736358 437 4.289 4.521 3.771 -2.486 -1.831 -2.402 0.9746370552 439 4.289 4.529 3.771 -2.486 -1.831 -2.402 0.9746293650 441 4.289 4.528 3.771 -2.486 -1.831 -2.402 0.9746289999 453 4.289 4.528 3.809 -2.486 -1.831 -2.402 0.9746278230 457 4.289 4.528 3.802 -2.486 -1.831 -2.402 0.9746270160 459 4.289 4.528 3.804 -2.486 -1.831 -2.402 0.9746263970 460 4.289 4.528 3.805 -2.486 -1.831 -2.402 0.9746263515 473 4.289 4.528 3.806 -2.485 -1.831 -2.402 0.9746262700 480 4.289 4.528 3.806 -2.485 -1.831 -2.020 0.9745187695 486 4.289 4.528 3.806 -2.485 -1.831 -2.039 0.9744831544 488 4.289 4.528 3.806 -2.485 -1.831 -2.038 0.9744828994 489 4.289 4.528 3.806 -2.485 -1.831 -2.036 0.9744828165 498 4.262 4.569 3.734 -2.486 -1.773 -2.007 0.9744106303 499 4.263 4.568 3.735 -2.486 -1.774 -2.007 0.9744082592 500 4.272 4.554 3.761 -2.486 -1.795 -2.018 0.9743546856 501 4.278 4.544 3.778 -2.486 -1.809 -2.025 0.9743387010 503 4.276 4.547 3.773 -2.486 -1.804 -2.023 0.9743347197 powell nthiter 5: fret = 0.974335 513 4.087 4.547 3.773 -2.486 -1.804 -2.023 0.9739135053 516 4.112 4.547 3.773 -2.486 -1.804 -2.023 0.9738252092 517 4.118 4.547 3.773 -2.486 -1.804 -2.023 0.9738192371 518 4.121 4.547 3.773 -2.486 -1.804 -2.023 0.9738176648 530 4.121 4.551 3.773 -2.486 -1.804 -2.023 0.9738167237 531 4.121 4.550 3.773 -2.486 -1.804 -2.023 0.9738167200 542 4.121 4.550 3.780 -2.486 -1.804 -2.023 0.9738073690 552 4.121 4.550 3.780 -2.487 -1.804 -2.023 0.9738062934 553 4.121 4.550 3.780 -2.506 -1.804 -2.023 0.9737913456 557 4.121 4.550 3.780 -2.505 -1.804 -2.023 0.9737912180 567 4.121 4.550 3.780 -2.505 -1.804 -2.027 0.9737907296 568 4.121 4.550 3.780 -2.505 -1.804 -2.026 0.9737902212 569 4.121 4.550 3.780 -2.505 -1.804 -2.025 0.9737901096 579 4.123 4.547 3.784 -2.505 -1.808 -2.027 0.9737828706 581 4.124 4.545 3.788 -2.505 -1.811 -2.028 0.9737798808 593 4.125 4.545 3.788 -2.505 -1.811 -2.028 0.9737794659 594 4.126 4.545 3.788 -2.504 -1.811 -2.028 0.9737794484 595 4.126 4.545 3.788 -2.505 -1.811 -2.028 0.9737794369 powell nthiter 6: fret = 0.973779 607 4.126 4.544 3.789 -2.505 -1.812 -2.029 0.9737793331 631 4.126 4.544 3.788 -2.505 -1.812 -2.029 0.9737792295 642 4.126 4.544 3.788 -2.511 -1.812 -2.029 0.9737791236 643 4.126 4.544 3.788 -2.508 -1.812 -2.029 0.9737775408 654 4.126 4.544 3.788 -2.508 -1.812 -2.027 0.9737770026 665 4.127 4.544 3.788 -2.508 -1.812 -2.027 0.9737769296 666 4.127 4.544 3.788 -2.508 -1.812 -2.027 0.9737769294 powell nthiter 7: fret = 0.973777 680 4.128 4.542 3.792 -2.508 -1.815 -2.029 0.9737752585 681 4.128 4.542 3.791 -2.508 -1.814 -2.028 0.9737750691 682 4.128 4.543 3.790 -2.508 -1.814 -2.028 0.9737750546 706 4.128 4.543 3.791 -2.508 -1.814 -2.028 0.9737748390 707 4.128 4.543 3.792 -2.508 -1.814 -2.028 0.9737748069 722 4.128 4.543 3.792 -2.510 -1.814 -2.028 0.9737745783 724 4.128 4.543 3.792 -2.509 -1.814 -2.028 0.9737744348 733 4.128 4.543 3.792 -2.509 -1.814 -2.027 0.9737742528 743 4.129 4.543 3.792 -2.509 -1.814 -2.027 0.9737739530 745 4.129 4.543 3.792 -2.509 -1.814 -2.027 0.9737739367 749 4.132 4.541 3.797 -2.510 -1.815 -2.027 0.9737724499 752 4.135 4.539 3.804 -2.512 -1.819 -2.027 0.9737720203 753 4.134 4.540 3.801 -2.512 -1.818 -2.027 0.9737715182 759 4.134 4.540 3.801 -2.512 -1.817 -2.027 0.9737715103 765 4.134 4.540 3.801 -2.512 -1.817 -2.027 0.9737715101 766 4.134 4.540 3.801 -2.512 -1.817 -2.027 0.9737714993 powell nthiter 8: fret = 0.973772 789 4.134 4.539 3.801 -2.512 -1.817 -2.027 0.9737712013 800 4.134 4.539 3.796 -2.512 -1.817 -2.027 0.9737706058 801 4.134 4.539 3.797 -2.512 -1.817 -2.027 0.9737701306 802 4.134 4.539 3.798 -2.512 -1.817 -2.027 0.9737699869 812 4.134 4.539 3.798 -2.533 -1.817 -2.027 0.9737660693 814 4.134 4.539 3.798 -2.529 -1.817 -2.027 0.9737657713 815 4.134 4.539 3.798 -2.528 -1.817 -2.027 0.9737655782 816 4.134 4.539 3.798 -2.522 -1.817 -2.027 0.9737651472 817 4.134 4.539 3.798 -2.524 -1.817 -2.027 0.9737650359 829 4.134 4.539 3.798 -2.524 -1.817 -2.023 0.9737629074 833 4.136 4.538 3.802 -2.525 -1.819 -2.023 0.9737579965 836 4.137 4.537 3.805 -2.526 -1.821 -2.023 0.9737569193 838 4.137 4.537 3.806 -2.526 -1.821 -2.023 0.9737568338 840 4.138 4.537 3.806 -2.526 -1.821 -2.023 0.9737568284 847 4.146 4.531 3.819 -2.542 -1.828 -2.019 0.9737532060 854 4.146 4.530 3.820 -2.543 -1.828 -2.018 0.9737530852 855 4.146 4.530 3.820 -2.543 -1.828 -2.018 0.9737530599 859 4.146 4.530 3.820 -2.543 -1.828 -2.018 0.9737530461 861 4.146 4.530 3.820 -2.543 -1.828 -2.018 0.9737530169 powell nthiter 9: fret = 0.973753 873 4.142 4.530 3.820 -2.544 -1.828 -2.019 0.9737523676 874 4.143 4.530 3.820 -2.544 -1.828 -2.019 0.9737519112 875 4.144 4.530 3.820 -2.544 -1.828 -2.019 0.9737517232 889 4.144 4.533 3.820 -2.544 -1.828 -2.019 0.9737505985 900 4.144 4.533 3.808 -2.544 -1.828 -2.019 0.9737478685 903 4.144 4.533 3.802 -2.544 -1.828 -2.019 0.9737444493 904 4.144 4.533 3.797 -2.544 -1.828 -2.019 0.9737443227 905 4.144 4.533 3.799 -2.544 -1.828 -2.019 0.9737437561 917 4.144 4.533 3.799 -2.545 -1.828 -2.019 0.9737432185 919 4.144 4.533 3.799 -2.547 -1.828 -2.019 0.9737429912 929 4.144 4.533 3.799 -2.547 -1.828 -2.016 0.9737393019 932 4.144 4.533 3.799 -2.547 -1.828 -2.012 0.9737370919 940 4.147 4.530 3.804 -2.553 -1.831 -2.011 0.9737318237 942 4.149 4.529 3.807 -2.557 -1.833 -2.010 0.9737315615 943 4.148 4.529 3.806 -2.555 -1.832 -2.010 0.9737311032 powell nthiter 10: fret = 0.973731 958 4.148 4.529 3.806 -2.555 -1.832 -2.010 0.9737309403 959 4.162 4.530 3.805 -2.553 -1.831 -2.010 0.9737280074 961 4.156 4.530 3.805 -2.554 -1.832 -2.010 0.9737253140 962 4.156 4.530 3.805 -2.554 -1.832 -2.010 0.9737252621 976 4.156 4.531 3.805 -2.554 -1.832 -2.010 0.9737249627 988 4.156 4.531 3.801 -2.554 -1.832 -2.010 0.9737219685 1012 4.156 4.531 3.801 -2.554 -1.832 -2.013 0.9737219189 1014 4.156 4.531 3.801 -2.554 -1.832 -2.012 0.9737218114 1021 4.157 4.530 3.802 -2.555 -1.832 -2.012 0.9737215131 1022 4.157 4.530 3.803 -2.556 -1.832 -2.011 0.9737214348 1023 4.157 4.530 3.802 -2.556 -1.832 -2.011 0.9737214067 powell nthiter 11: fret = 0.973721 1038 4.158 4.530 3.802 -2.556 -1.832 -2.011 0.9737213567 1040 4.158 4.530 3.802 -2.556 -1.832 -2.011 0.9737213513 1052 4.158 4.529 3.802 -2.556 -1.832 -2.011 0.9737211285 1063 4.158 4.529 3.801 -2.556 -1.832 -2.011 0.9737209562 1087 4.158 4.529 3.801 -2.556 -1.832 -2.012 0.9737208943 1094 4.158 4.529 3.801 -2.556 -1.832 -2.012 0.9737208682 1096 4.158 4.529 3.802 -2.557 -1.833 -2.012 0.9737207529 1098 4.158 4.528 3.803 -2.557 -1.833 -2.012 0.9737207017 1100 4.158 4.529 3.802 -2.557 -1.833 -2.012 0.9737206857 powell nthiter 12: fret = 0.973721 1113 4.158 4.529 3.802 -2.557 -1.833 -2.012 0.9737206840 1114 4.157 4.529 3.802 -2.557 -1.833 -2.012 0.9737206469 1116 4.157 4.529 3.802 -2.557 -1.833 -2.012 0.9737206362 1153 4.157 4.529 3.802 -2.556 -1.833 -2.012 0.9737205134 1165 4.157 4.529 3.802 -2.556 -1.833 -2.013 0.9737204607 1173 4.158 4.528 3.804 -2.557 -1.833 -2.013 0.9737203337 1179 4.158 4.528 3.804 -2.557 -1.833 -2.013 0.9737203225 powell nthiter 13: fret = 0.973720 1218 4.158 4.527 3.802 -2.557 -1.833 -2.013 0.9737201122 1252 4.158 4.527 3.803 -2.558 -1.834 -2.014 0.9737199657 1254 4.158 4.527 3.803 -2.559 -1.834 -2.013 0.9737198458 powell nthiter 14: fret = 0.973720 1267 4.158 4.527 3.803 -2.559 -1.834 -2.013 0.9737198392 Powell done niters = 14 Computing relative cost 0 -25.0 -25.0 -25.0 1.009574 1 -25.0 -25.0 25.0 1.033591 2 -25.0 25.0 -25.0 1.018845 3 -25.0 25.0 25.0 1.015683 4 25.0 -25.0 -25.0 1.038104 5 25.0 -25.0 25.0 1.048356 6 25.0 25.0 -25.0 1.022471 7 25.0 25.0 25.0 1.041853 REL: 8 0.973720 8.228477 1.028560 rel = 0.946683 Number of iterations 14 Min cost was 0.973720 Number of FunctionCalls 1334 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 67.023940 sec Parameters at optimum (transmm) 4.15814 4.52656 3.80323 Parameters at optimum (rotdeg) -2.55875 -1.83414 -2.01339 Final costs ---------------- Number of surface hits 253432 WM Intensity 293.6132 +/- 125.1986 Ctx Intensity 297.9291 +/- 124.8658 Pct Contrast 1.5292 +/- 42.5985 Cost 0.9737 RelCost 1.0184 Reg at min cost was -0.03510 0.99892 -0.03050 0.64652; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01603; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/register.dof6.dat, type = 14 Original Reg -0.06933 0.99759 0.00245 -3.76985; 0.99499 0.06932 -0.07208 4.04924; 0.07208 0.00256 0.99740 -3.49112; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.03423 -0.00133 0.03294 -4.41638; -0.00408 0.03503 -0.04565 -4.49252; 0.04672 -0.02883 -0.00179 -3.50715; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 7.928505 Computing change in rh position Surface-RMS-Diff-mm 8.010794 0.616584 9.713605 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done MinCost: 0.973720 293.613165 297.929114 1.529228 tkregister2_cmdl --mov bold/template.nii.gz --reg bold/register.dof6.dat --noedit --ltaout bold/register.dof6.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/template.nii.gz reg file bold/register.dof6.dat LoadVol 0 ZeroCRAS 0 7.4.1 Diagnostic Level -1 ---- Input registration matrix -------- -0.03510 0.99892 -0.03050 0.64652; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01603; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/template.nii.gz Tmov: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -88.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -0.03510 0.99892 -0.03050 0.64652; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01603; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = 20240801_dw204 RegMat --------------------------- -0.03510 0.99892 -0.03050 0.64652; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01603; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue Jun 17 12:52:01 EDT 2025 Ended at Tue Jun 17 12:53:55 EDT 2025 BBR-Run-Time-Sec 114 bbregister Done To check results, run: tkregisterfv --mov bold/template.nii.gz --reg bold/register.dof6.lta --surfs --sd /Volumes/umms-hillmera/asem_ptsd/DW204 Run: 002 ---------------- Tue Jun 17 12:53:55 EDT 2025 -------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 bbregister --s 20240801_dw204 --init-coreg --6 --bold --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --lta bold/002/register.dof6.lta --init-reg-out bold/002/init.register.dof6.dat tmp bold/002/tmp.bbregister.89683 Log file is bold/002/register.dof6.log Tue Jun 17 12:53:55 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 /Applications/freesurfer/bin/bbregister --s 20240801_dw204 --init-coreg --6 --bold --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --lta bold/002/register.dof6.lta --init-reg-out bold/002/init.register.dof6.dat FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 FREESURFER_HOME /Applications/freesurfer mri_convert bold/002/template.nii.gz bold/002/tmp.bbregister.89683/template.nii mri_convert bold/002/template.nii.gz bold/002/tmp.bbregister.89683/template.nii reading from bold/002/template.nii.gz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to bold/002/tmp.bbregister.89683/template.nii... mri_coreg --s 20240801_dw204 --mov bold/002/tmp.bbregister.89683/template.nii --regdat bold/002/tmp.bbregister.89683/reg.init.dat --reg bold/002/tmp.bbregister.89683/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 cmdline mri_coreg --s 20240801_dw204 --mov bold/002/tmp.bbregister.89683/template.nii --regdat bold/002/tmp.bbregister.89683/reg.init.dat --reg bold/002/tmp.bbregister.89683/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov bold/002/tmp.bbregister.89683/template.nii Reading in ref /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/brainmask.mgz Reading in and applying refmask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz Setting cras translation parameters to align volume centers Init matrix params -1.0000 0.0000 -1.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 1.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 1.00000; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt -1.0000 0.0000 -1.0000 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 1199.0000 mov gstd 1.8914 1.8914 1.8914 Smoothing mov refsat = 116.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0315854939 nhits = 179166 out of 16777216, Percent Overlap: 68.3 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -1.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 -1.00000; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.00000 0.00000 -1.00000 255.00000; 0.00000 1.00000 0.00000 0.00000; -1.00000 0.00000 0.00000 215.00000; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -1.00000 0.00000 -1.00000 0.00000 0.00000 0.00000 -1.0287818 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: -1.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0315854549 #@# 4 188 -1.00000 0.00000 -1.00000 0.00000 0.00000 0.00000 -1.0315855 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.031585 #@# 4 190 0.00000 0.00000 -1.00000 0.00000 0.00000 0.00000 -1.0326102 #@# 4 195 -0.03725 0.00000 -1.00000 0.00000 0.00000 0.00000 -1.0326129 #@# 4 196 -0.04725 0.00000 -1.00000 0.00000 0.00000 0.00000 -1.0326132 #@# 4 204 -0.04725 -0.04875 -1.00000 0.00000 0.00000 0.00000 -1.0326172 #@# 4 205 -0.04725 -0.09278 -1.00000 0.00000 0.00000 0.00000 -1.0326179 #@# 4 206 -0.04725 -0.08204 -1.00000 0.00000 0.00000 0.00000 -1.0326182 #@# 4 214 -0.04725 -0.07204 -0.61803 0.00000 0.00000 0.00000 -1.0327752 #@# 4 226 -0.04725 -0.07204 -0.59803 -0.05116 0.00000 0.00000 -1.0327843 #@# 4 228 -0.04725 -0.07204 -0.59803 -0.11762 0.00000 0.00000 -1.0327885 #@# 4 229 -0.04725 -0.07204 -0.59803 -0.10762 0.00000 0.00000 -1.0327886 #@# 4 246 -0.04725 -0.07204 -0.59803 -0.10762 -0.01239 -0.01000 -1.0327888 powell nthiter 1: fret = -1.032789 #@# 4 255 -0.03374 -0.07204 -0.59803 -0.10762 -0.01239 -0.01000 -1.0327892 #@# 4 263 -0.03374 -0.00521 -0.59803 -0.10762 -0.01239 -0.01000 -1.0327957 #@# 4 273 -0.03374 -0.00521 -0.64797 -0.10762 -0.01239 -0.01000 -1.0327982 #@# 4 282 -0.03374 -0.00521 -0.63797 -0.11762 -0.01239 -0.01000 -1.0327984 #@# 4 300 -0.03374 -0.00521 -0.63797 -0.13427 -0.01239 -0.02000 -1.0327985 Powell done niters total = 1 OptTimeSec 5.3 sec OptTimeMin 0.09 min nEvals 301 Final optimized parameters -0.03373676 -0.00521132 -0.63796526 -0.13427094 -0.01238912 -0.02000000 Final matrix parameters -0.0337 -0.0052 -0.6380 -0.1343 -0.0124 -0.0300 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.032798579752070 --------------------------------- Final RefRAS-to-MovRAS 1.00000 -0.00035 -0.00022 -0.03374; 0.00035 1.00000 -0.00234 -0.00521; 0.00022 0.00234 1.00000 -0.63797; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.00035 -0.00234 -1.00000 255.26440; 0.00022 1.00000 -0.00234 -0.16085; -1.00000 0.00022 -0.00035 215.97224; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters -0.0337 -0.0052 -0.6380 -0.1343 -0.0124 -0.0200 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters -0.0337 -0.0052 -0.6380 -0.1343 -0.0124 -0.0200 nhits = 178404 out of 16777216, Percent Overlap: 68.1 mri_coreg RunTimeSec 38.0 sec To check run: tkregisterfv --mov bold/002/tmp.bbregister.89683/template.nii --targ /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/brainmask.mgz --reg bold/002/tmp.bbregister.89683/mri_coreg.lta --s 20240801_dw204 --surfs mri_coreg done mri_segreg --mov bold/002/tmp.bbregister.89683/template.nii --init-reg bold/002/tmp.bbregister.89683/reg.init.dat --out-reg bold/002/tmp.bbregister.89683/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 mri_segreg --mov bold/002/tmp.bbregister.89683/template.nii --init-reg bold/002/tmp.bbregister.89683/reg.init.dat --out-reg bold/002/tmp.bbregister.89683/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/002/tmp.bbregister.89683/template.nii regfile bold/002/tmp.bbregister.89683/reg.init.dat subject 20240801_dw204 dof 6 outregfile bold/002/tmp.bbregister.89683/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750665457 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.00035 1.00000 -0.00234 0.99059; 1.00000 -0.00035 -0.00022 -0.04475; 0.00022 0.00234 1.00000 0.43340; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.031526 1 -25.0 -25.0 25.0 1.047528 2 -25.0 25.0 -25.0 0.993458 3 -25.0 25.0 25.0 1.017234 4 25.0 -25.0 -25.0 1.053308 5 25.0 -25.0 25.0 1.037679 6 25.0 25.0 -25.0 1.056287 7 25.0 25.0 25.0 0.993897 REL: 8 1.937984 8.230918 1.028865 rel = 1.88361 Initial costs ---------------- Number of surface hits 2538 WM Intensity 392.4088 +/- 79.1836 Ctx Intensity 260.6141 +/- 54.4622 Pct Contrast -40.0498 +/- 17.8701 Cost 1.9380 RelCost 1.8836 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0542 1.0542 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0540 1.0540 0.0 9 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 -4.0000 1.0527 1.0527 0.0 12 -4.0000 -4.0000 -4.0000 0.0000 0.0000 -4.0000 1.0425 1.0425 0.0 13 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.0000 1.0265 1.0265 0.0 94 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.0000 1.0179 1.0179 0.0 185 -4.0000 4.0000 -4.0000 4.0000 0.0000 4.0000 1.0157 1.0157 0.0 Brute Force -------------------------- Min cost was 1.015726 Number of iterations 729 Search time 0.872203 sec Parameters at best (transmm, rotdeg) -4.000 4.000 -4.000 4.000 0.000 4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -4 1 4 2 -4 3 4 4 0 5 4 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 1.015726 5 -4.618 4.000 -4.000 4.000 0.000 4.000 1.0108893622 8 -4.764 4.000 -4.000 4.000 0.000 4.000 1.0064498007 12 -4.765 4.000 -4.000 4.000 0.000 4.000 1.0064428948 13 -4.769 4.000 -4.000 4.000 0.000 4.000 1.0064281301 15 -4.770 4.000 -4.000 4.000 0.000 4.000 1.0064277553 25 -4.770 4.052 -4.000 4.000 0.000 4.000 1.0060640775 27 -4.770 4.049 -4.000 4.000 0.000 4.000 1.0060591880 49 -4.770 4.049 -4.000 4.055 0.000 4.000 1.0044269396 51 -4.770 4.049 -4.000 4.056 0.000 4.000 1.0044235846 52 -4.770 4.049 -4.000 4.057 0.000 4.000 1.0044223544 61 -4.770 4.049 -4.000 4.057 0.007 4.000 1.0042814651 64 -4.770 4.049 -4.000 4.057 0.020 4.000 1.0042003072 65 -4.770 4.049 -4.000 4.057 0.019 4.000 1.0041980141 66 -4.770 4.049 -4.000 4.057 0.018 4.000 1.0041961108 68 -4.770 4.049 -4.000 4.057 0.017 4.000 1.0041949962 79 -4.770 4.049 -4.000 4.057 0.017 4.017 1.0040195954 80 -4.770 4.049 -4.000 4.057 0.017 4.013 1.0040017249 powell nthiter 1: fret = 1.004002 94 -4.774 4.049 -4.000 4.057 0.017 4.013 1.0039991326 95 -4.773 4.049 -4.000 4.057 0.017 4.013 1.0039986513 96 -4.772 4.049 -4.000 4.057 0.017 4.013 1.0039982514 106 -4.772 4.056 -4.000 4.057 0.017 4.013 1.0039661195 108 -4.772 4.055 -4.000 4.057 0.017 4.013 1.0039639892 119 -4.772 4.055 -3.961 4.057 0.017 4.013 1.0034739404 122 -4.772 4.055 -3.962 4.057 0.017 4.013 1.0034739315 131 -4.772 4.055 -3.962 4.099 0.017 4.013 1.0031020612 135 -4.772 4.055 -3.962 4.102 0.017 4.013 1.0030887978 137 -4.772 4.055 -3.962 4.103 0.017 4.013 1.0030886738 145 -4.772 4.055 -3.962 4.103 0.000 4.013 1.0030606529 147 -4.772 4.055 -3.962 4.103 0.007 4.013 1.0030303853 148 -4.772 4.055 -3.962 4.103 0.008 4.013 1.0030299515 powell nthiter 2: fret = 1.003030 172 -4.758 4.055 -3.962 4.103 0.008 4.013 1.0030049103 174 -4.764 4.055 -3.962 4.103 0.008 4.013 1.0029631359 186 -4.764 4.056 -3.962 4.103 0.008 4.013 1.0029580979 187 -4.764 4.058 -3.962 4.103 0.008 4.013 1.0029519914 199 -4.764 4.058 -3.936 4.103 0.008 4.013 1.0025955556 200 -4.764 4.058 -3.935 4.103 0.008 4.013 1.0025893059 202 -4.764 4.058 -3.931 4.103 0.008 4.013 1.0025772365 203 -4.764 4.058 -3.930 4.103 0.008 4.013 1.0025761674 204 -4.764 4.058 -3.929 4.103 0.008 4.013 1.0025758890 214 -4.764 4.058 -3.929 4.107 0.008 4.013 1.0024975362 215 -4.764 4.058 -3.929 4.121 0.008 4.013 1.0023449705 220 -4.764 4.058 -3.929 4.123 0.008 4.013 1.0023378472 221 -4.764 4.058 -3.929 4.124 0.008 4.013 1.0023376089 229 -4.764 4.058 -3.929 4.124 -0.009 4.013 1.0021966702 233 -4.764 4.058 -3.929 4.124 -0.010 4.013 1.0021951609 234 -4.764 4.058 -3.929 4.124 -0.011 4.013 1.0021949547 244 -4.764 4.058 -3.929 4.124 -0.011 4.010 1.0021729741 246 -4.764 4.058 -3.929 4.124 -0.011 4.008 1.0021644227 247 -4.764 4.058 -3.929 4.124 -0.011 4.007 1.0021638596 powell nthiter 3: fret = 1.002164 263 -4.763 4.058 -3.929 4.124 -0.011 4.007 1.0021607316 276 -4.763 4.056 -3.929 4.124 -0.011 4.007 1.0021552825 287 -4.763 4.056 -3.928 4.124 -0.011 4.007 1.0021384585 288 -4.763 4.056 -3.919 4.124 -0.011 4.007 1.0020907308 290 -4.763 4.056 -3.921 4.124 -0.011 4.007 1.0020904075 292 -4.763 4.056 -3.920 4.124 -0.011 4.007 1.0020894278 302 -4.763 4.056 -3.920 4.119 -0.011 4.007 1.0020872253 303 -4.763 4.056 -3.920 4.121 -0.011 4.007 1.0020834128 314 -4.763 4.056 -3.920 4.121 -0.015 4.007 1.0020773493 315 -4.763 4.056 -3.920 4.121 -0.014 4.007 1.0020771304 329 -4.763 4.056 -3.920 4.121 -0.014 4.005 1.0020726010 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.017596 1 -25.0 -25.0 25.0 1.036536 2 -25.0 25.0 -25.0 1.015611 3 -25.0 25.0 25.0 1.034368 4 25.0 -25.0 -25.0 1.020799 5 25.0 -25.0 25.0 1.051545 6 25.0 25.0 -25.0 1.055021 7 25.0 25.0 25.0 1.022751 REL: 8 1.002073 8.254226 1.031778 rel = 0.971209 Number of iterations 3 Min cost was 1.002073 Number of FunctionCalls 331 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.400997 sec Parameters at optimum (transmm) -4.76321 4.05565 -3.92043 Parameters at optimum (rotdeg) 4.12082 -0.01435 4.00480 Final costs ---------------- Number of surface hits 2538 WM Intensity 302.9852 +/- 112.1439 Ctx Intensity 301.7366 +/- 116.3660 Pct Contrast -1.4851 +/- 41.3728 Cost 1.0021 RelCost 1.8836 Reg at min cost was -0.06933 0.99759 0.00245 -3.76985; 0.99499 0.06932 -0.07208 4.04924; 0.07208 0.00256 0.99740 -3.49112; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/002/tmp.bbregister.89683/bbr.pass1.dat, type = 14 Original Reg 0.00035 1.00000 -0.00234 0.99059; 1.00000 -0.00035 -0.00022 -0.04475; 0.00022 0.00234 1.00000 0.43340; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.06968 0.00241 -0.00479 4.76044; 0.00501 -0.06967 0.07186 -4.09398; -0.07186 -0.00022 0.00260 3.92452; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 7.490767 Computing change in rh position Surface-RMS-Diff-mm 7.614866 1.148211 11.105092 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov bold/002/tmp.bbregister.89683/template.nii --init-reg bold/002/tmp.bbregister.89683/bbr.pass1.dat --out-reg bold/002/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/002/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/002/tmp.bbregister.89683/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 mri_segreg --mov bold/002/tmp.bbregister.89683/template.nii --init-reg bold/002/tmp.bbregister.89683/bbr.pass1.dat --out-reg bold/002/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/002/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/002/tmp.bbregister.89683/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/002/tmp.bbregister.89683/template.nii regfile bold/002/tmp.bbregister.89683/bbr.pass1.dat subject 20240801_dw204 dof 6 outregfile bold/002/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750192503 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.06933 0.99759 0.00245 -3.76985; 0.99499 0.06932 -0.07208 4.04924; 0.07208 0.00256 0.99740 -3.49112; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.027868 1 -25.0 -25.0 25.0 1.043856 2 -25.0 25.0 -25.0 1.031360 3 -25.0 25.0 25.0 1.034708 4 25.0 -25.0 -25.0 1.032571 5 25.0 -25.0 25.0 1.015032 6 25.0 25.0 -25.0 1.039001 7 25.0 25.0 25.0 1.018414 REL: 8 1.049314 8.242809 1.030351 rel = 1.0184 Initial costs ---------------- Number of surface hits 253432 WM Intensity 307.3857 +/- 111.0625 Ctx Intensity 305.8452 +/- 115.8493 Pct Contrast -1.7254 +/- 40.9277 Cost 1.0493 RelCost 1.0184 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 1.0152 1.0152 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 1.0134 1.0134 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 1.0129 1.0129 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 1.0113 1.0113 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 1.0096 1.0096 0.0 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 1.0095 1.0095 0.0 40 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0000 1.0083 1.0083 0.0 52 -0.1000 -0.1000 0.0000 0.1000 0.1000 0.0000 1.0079 1.0079 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0063 1.0063 0.0 130 -0.1000 0.0000 0.0000 0.1000 0.0000 0.0000 1.0056 1.0056 0.0 215 -0.1000 0.1000 0.0000 0.1000 0.1000 0.1000 1.0035 1.0035 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0021 1.0021 0.0 Brute Force -------------------------- Min cost was 1.002073 Number of iterations 729 Search time 0.679498 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 1.049314 2 1.000 0.000 0.000 0.000 0.000 0.000 1.0425582378 5 1.618 0.000 0.000 0.000 0.000 0.000 1.0405346135 8 1.761 0.000 0.000 0.000 0.000 0.000 1.0403860276 10 1.703 0.000 0.000 0.000 0.000 0.000 1.0403128750 12 1.702 0.000 0.000 0.000 0.000 0.000 1.0403128121 18 1.701 0.000 0.000 0.000 0.000 0.000 1.0403127689 20 1.701 1.000 0.000 0.000 0.000 0.000 1.0394701013 21 1.701 2.618 0.000 0.000 0.000 0.000 1.0334044390 22 1.701 5.236 0.000 0.000 0.000 0.000 1.0305819580 23 1.701 4.782 0.000 0.000 0.000 0.000 1.0299212312 30 1.701 4.789 0.000 0.000 0.000 0.000 1.0298990207 31 1.701 4.808 0.000 0.000 0.000 0.000 1.0298602021 32 1.701 4.823 0.000 0.000 0.000 0.000 1.0298503477 33 1.701 4.822 0.000 0.000 0.000 0.000 1.0298496035 35 1.701 4.821 0.000 0.000 0.000 0.000 1.0298493158 38 1.701 4.821 1.000 0.000 0.000 0.000 1.0184644820 39 1.701 4.821 2.618 0.000 0.000 0.000 1.0175220701 40 1.701 4.821 1.880 0.000 0.000 0.000 1.0145558399 42 1.701 4.821 1.544 0.000 0.000 0.000 1.0143296688 44 1.701 4.821 1.679 0.000 0.000 0.000 1.0143169919 48 1.701 4.821 1.658 0.000 0.000 0.000 1.0142962736 50 1.701 4.821 1.662 0.000 0.000 0.000 1.0142955787 52 1.701 4.821 1.660 0.000 0.000 0.000 1.0142955586 56 1.701 4.821 1.660 -1.618 0.000 0.000 1.0076658029 60 1.701 4.821 1.660 -2.618 0.000 0.000 1.0059208093 65 1.701 4.821 1.660 -2.647 0.000 0.000 1.0058017903 66 1.701 4.821 1.660 -2.726 0.000 0.000 1.0057984528 67 1.701 4.821 1.660 -2.687 0.000 0.000 1.0057678330 68 1.701 4.821 1.660 -2.688 0.000 0.000 1.0057674254 69 1.701 4.821 1.660 -2.693 0.000 0.000 1.0057649648 70 1.701 4.821 1.660 -2.706 0.000 0.000 1.0057589965 72 1.701 4.821 1.660 -2.703 0.000 0.000 1.0057584633 73 1.701 4.821 1.660 -2.704 0.000 0.000 1.0057583062 82 1.701 4.821 1.660 -2.704 -0.052 0.000 1.0056586517 84 1.701 4.821 1.660 -2.704 -0.049 0.000 1.0056573977 86 1.701 4.821 1.660 -2.704 -0.048 0.000 1.0056573439 92 1.701 4.821 1.660 -2.704 -0.048 -0.618 1.0055623767 94 1.701 4.821 1.660 -2.704 -0.048 -0.323 1.0050363090 95 1.701 4.821 1.660 -2.704 -0.048 -0.322 1.0050307356 96 1.701 4.821 1.660 -2.704 -0.048 -0.199 1.0047273305 99 1.701 4.821 1.660 -2.704 -0.048 -0.168 1.0047097698 103 1.701 4.821 1.660 -2.704 -0.048 -0.166 1.0047083269 powell nthiter 1: fret = 1.004708 108 2.701 4.821 1.660 -2.704 -0.048 -0.166 1.0027624557 111 3.319 4.821 1.660 -2.704 -0.048 -0.166 1.0026303264 113 3.026 4.821 1.660 -2.704 -0.048 -0.166 1.0023752238 114 3.042 4.821 1.660 -2.704 -0.048 -0.166 1.0023476357 115 3.126 4.821 1.660 -2.704 -0.048 -0.166 1.0022096652 117 3.158 4.821 1.660 -2.704 -0.048 -0.166 1.0021338127 118 3.162 4.821 1.660 -2.704 -0.048 -0.166 1.0021292068 120 3.168 4.821 1.660 -2.704 -0.048 -0.166 1.0021246784 125 3.168 5.821 1.660 -2.704 -0.048 -0.166 1.0008376491 129 3.168 5.439 1.660 -2.704 -0.048 -0.166 0.9997791133 132 3.168 5.412 1.660 -2.704 -0.048 -0.166 0.9997473296 138 3.168 5.415 1.660 -2.704 -0.048 -0.166 0.9997450836 142 3.168 5.415 2.660 -2.704 -0.048 -0.166 0.9975964869 146 3.168 5.415 2.278 -2.704 -0.048 -0.166 0.9963778716 149 3.168 5.415 2.203 -2.704 -0.048 -0.166 0.9963215111 151 3.168 5.415 2.233 -2.704 -0.048 -0.166 0.9962248670 154 3.168 5.415 2.234 -2.704 -0.048 -0.166 0.9962244950 162 3.168 5.415 2.235 -2.829 -0.048 -0.166 0.9961014322 163 3.168 5.415 2.235 -2.861 -0.048 -0.166 0.9961006639 168 3.168 5.415 2.235 -2.871 -0.048 -0.166 0.9960954605 176 3.168 5.415 2.235 -2.870 -0.666 -0.166 0.9938030914 178 3.168 5.415 2.235 -2.870 -0.516 -0.166 0.9937327659 179 3.168 5.415 2.235 -2.870 -0.565 -0.166 0.9937080203 180 3.168 5.415 2.235 -2.870 -0.567 -0.166 0.9937030636 182 3.168 5.415 2.235 -2.870 -0.582 -0.166 0.9936984288 183 3.168 5.415 2.235 -2.870 -0.575 -0.166 0.9936955853 186 3.168 5.415 2.235 -2.870 -0.574 -0.166 0.9936954171 187 3.168 5.415 2.235 -2.870 -0.573 -0.166 0.9936953971 192 3.168 5.415 2.235 -2.870 -0.573 -0.784 0.9920963676 198 3.168 5.415 2.235 -2.870 -0.573 -0.790 0.9920934094 powell nthiter 2: fret = 0.992093 210 3.550 5.415 2.235 -2.870 -0.573 -0.791 0.9916388562 211 3.536 5.415 2.235 -2.870 -0.573 -0.791 0.9916043419 213 3.491 5.415 2.235 -2.870 -0.573 -0.791 0.9914728254 215 3.484 5.415 2.235 -2.870 -0.573 -0.791 0.9914662401 216 3.481 5.415 2.235 -2.870 -0.573 -0.791 0.9914652394 217 3.479 5.415 2.235 -2.870 -0.573 -0.791 0.9914648069 224 3.479 4.797 2.235 -2.870 -0.573 -0.791 0.9899755524 226 3.479 4.987 2.235 -2.870 -0.573 -0.791 0.9892000267 228 3.479 4.944 2.235 -2.870 -0.573 -0.791 0.9891015070 229 3.479 4.927 2.235 -2.870 -0.573 -0.791 0.9890892444 231 3.479 4.933 2.235 -2.870 -0.573 -0.791 0.9890862342 232 3.479 4.932 2.235 -2.870 -0.573 -0.791 0.9890860383 235 3.479 4.932 3.235 -2.870 -0.573 -0.791 0.9876035172 239 3.479 4.932 2.853 -2.870 -0.573 -0.791 0.9874969698 240 3.479 4.932 3.028 -2.870 -0.573 -0.791 0.9874059176 242 3.479 4.932 3.107 -2.870 -0.573 -0.791 0.9873263860 243 3.479 4.932 3.095 -2.870 -0.573 -0.791 0.9873093894 244 3.479 4.932 3.082 -2.870 -0.573 -0.791 0.9873023751 246 3.479 4.932 3.086 -2.870 -0.573 -0.791 0.9873007114 248 3.479 4.932 3.085 -2.870 -0.573 -0.791 0.9873005754 263 3.479 4.932 3.085 -2.867 -0.573 -0.791 0.9872997725 272 3.479 4.932 3.085 -2.865 -1.191 -0.791 0.9825817425 275 3.479 4.932 3.085 -2.865 -1.211 -0.791 0.9825752935 276 3.479 4.932 3.085 -2.865 -1.222 -0.791 0.9825532439 277 3.479 4.932 3.085 -2.865 -1.248 -0.791 0.9824697604 278 3.479 4.932 3.085 -2.865 -1.264 -0.791 0.9824625159 279 3.479 4.932 3.085 -2.865 -1.259 -0.791 0.9824548937 282 3.479 4.932 3.085 -2.865 -1.258 -0.791 0.9824547453 287 3.479 4.932 3.085 -2.865 -1.258 -1.409 0.9822324794 289 3.479 4.932 3.085 -2.865 -1.258 -1.197 0.9811880963 290 3.479 4.932 3.085 -2.865 -1.258 -1.114 0.9809479105 293 3.479 4.932 3.085 -2.865 -1.258 -1.126 0.9809168387 296 3.479 4.932 3.085 -2.865 -1.258 -1.129 0.9809125557 297 3.479 4.932 3.085 -2.865 -1.258 -1.131 0.9809122830 299 3.790 4.448 3.935 -2.860 -1.943 -1.470 0.9778431833 305 3.671 4.633 3.611 -2.862 -1.681 -1.340 0.9776454533 306 3.723 4.553 3.752 -2.861 -1.795 -1.397 0.9771949016 307 3.725 4.549 3.758 -2.861 -1.800 -1.399 0.9771755812 309 3.730 4.541 3.773 -2.861 -1.812 -1.405 0.9771647912 310 3.729 4.543 3.769 -2.861 -1.809 -1.404 0.9771625621 powell nthiter 3: fret = 0.977163 322 3.732 4.543 3.769 -2.861 -1.809 -1.404 0.9771611809 324 3.734 4.543 3.769 -2.861 -1.809 -1.404 0.9771611215 332 3.734 4.659 3.769 -2.861 -1.809 -1.404 0.9765374912 333 3.734 4.693 3.769 -2.861 -1.809 -1.404 0.9765203613 336 3.734 4.727 3.769 -2.861 -1.809 -1.404 0.9764378216 337 3.734 4.748 3.769 -2.861 -1.809 -1.404 0.9764374867 338 3.734 4.738 3.769 -2.861 -1.809 -1.404 0.9764338839 339 3.734 4.739 3.769 -2.861 -1.809 -1.404 0.9764329382 340 3.734 4.742 3.769 -2.861 -1.809 -1.404 0.9764307363 343 3.734 4.743 3.769 -2.861 -1.809 -1.404 0.9764304543 350 3.734 4.743 3.686 -2.861 -1.809 -1.404 0.9764145041 351 3.734 4.743 3.719 -2.861 -1.809 -1.404 0.9763850894 352 3.734 4.743 3.723 -2.861 -1.809 -1.404 0.9763847711 354 3.734 4.743 3.741 -2.861 -1.809 -1.404 0.9763756603 358 3.734 4.743 3.742 -2.861 -1.809 -1.404 0.9763754524 359 3.734 4.743 3.743 -2.861 -1.809 -1.404 0.9763754105 365 3.734 4.743 3.743 -2.479 -1.809 -1.404 0.9761646049 373 3.734 4.743 3.743 -2.489 -1.809 -1.404 0.9761553135 375 3.734 4.743 3.743 -2.488 -1.809 -1.404 0.9761547904 377 3.734 4.743 3.743 -2.487 -1.809 -1.404 0.9761546885 383 3.734 4.743 3.743 -2.487 -1.809 -2.022 0.9754989718 384 3.734 4.743 3.743 -2.487 -1.809 -2.404 0.9753514382 389 3.734 4.743 3.743 -2.487 -1.809 -2.390 0.9753154019 392 3.734 4.743 3.743 -2.487 -1.809 -2.391 0.9753153704 400 3.754 4.711 3.798 -2.486 -1.854 -2.413 0.9753039505 401 3.746 4.723 3.777 -2.486 -1.836 -2.405 0.9752356808 402 3.744 4.726 3.772 -2.486 -1.832 -2.402 0.9752338443 406 3.744 4.727 3.771 -2.486 -1.831 -2.402 0.9752337585 powell nthiter 4: fret = 0.975234 414 4.126 4.727 3.771 -2.486 -1.831 -2.402 0.9750910544 416 4.362 4.727 3.771 -2.486 -1.831 -2.402 0.9749830352 418 4.272 4.727 3.771 -2.486 -1.831 -2.402 0.9749700239 419 4.300 4.727 3.771 -2.486 -1.831 -2.402 0.9749526266 421 4.296 4.727 3.771 -2.486 -1.831 -2.402 0.9749501512 422 4.287 4.727 3.771 -2.486 -1.831 -2.402 0.9749467506 424 4.290 4.727 3.771 -2.486 -1.831 -2.402 0.9749463999 426 4.289 4.727 3.771 -2.486 -1.831 -2.402 0.9749463711 433 4.289 4.592 3.771 -2.486 -1.831 -2.402 0.9747513421 434 4.289 4.581 3.771 -2.486 -1.831 -2.402 0.9747300956 436 4.289 4.512 3.771 -2.486 -1.831 -2.402 0.9746736358 437 4.289 4.521 3.771 -2.486 -1.831 -2.402 0.9746370552 439 4.289 4.529 3.771 -2.486 -1.831 -2.402 0.9746293650 441 4.289 4.528 3.771 -2.486 -1.831 -2.402 0.9746289999 453 4.289 4.528 3.809 -2.486 -1.831 -2.402 0.9746278230 457 4.289 4.528 3.802 -2.486 -1.831 -2.402 0.9746270160 459 4.289 4.528 3.804 -2.486 -1.831 -2.402 0.9746263970 460 4.289 4.528 3.805 -2.486 -1.831 -2.402 0.9746263515 473 4.289 4.528 3.806 -2.485 -1.831 -2.402 0.9746262700 480 4.289 4.528 3.806 -2.485 -1.831 -2.020 0.9745187695 486 4.289 4.528 3.806 -2.485 -1.831 -2.039 0.9744831544 488 4.289 4.528 3.806 -2.485 -1.831 -2.038 0.9744828994 489 4.289 4.528 3.806 -2.485 -1.831 -2.036 0.9744828165 498 4.262 4.569 3.734 -2.486 -1.773 -2.007 0.9744106303 499 4.263 4.568 3.735 -2.486 -1.774 -2.007 0.9744082592 500 4.272 4.554 3.761 -2.486 -1.795 -2.018 0.9743546856 501 4.278 4.544 3.778 -2.486 -1.809 -2.025 0.9743387010 503 4.276 4.547 3.773 -2.486 -1.804 -2.023 0.9743347197 powell nthiter 5: fret = 0.974335 513 4.087 4.547 3.773 -2.486 -1.804 -2.023 0.9739135053 516 4.112 4.547 3.773 -2.486 -1.804 -2.023 0.9738252092 517 4.118 4.547 3.773 -2.486 -1.804 -2.023 0.9738192371 518 4.121 4.547 3.773 -2.486 -1.804 -2.023 0.9738176648 530 4.121 4.551 3.773 -2.486 -1.804 -2.023 0.9738167237 531 4.121 4.550 3.773 -2.486 -1.804 -2.023 0.9738167200 542 4.121 4.550 3.780 -2.486 -1.804 -2.023 0.9738073690 552 4.121 4.550 3.780 -2.487 -1.804 -2.023 0.9738062934 553 4.121 4.550 3.780 -2.506 -1.804 -2.023 0.9737913456 557 4.121 4.550 3.780 -2.505 -1.804 -2.023 0.9737912180 567 4.121 4.550 3.780 -2.505 -1.804 -2.027 0.9737907296 568 4.121 4.550 3.780 -2.505 -1.804 -2.026 0.9737902212 569 4.121 4.550 3.780 -2.505 -1.804 -2.025 0.9737901096 579 4.123 4.547 3.784 -2.505 -1.808 -2.027 0.9737828706 581 4.124 4.545 3.788 -2.505 -1.811 -2.028 0.9737798808 593 4.125 4.545 3.788 -2.505 -1.811 -2.028 0.9737794659 594 4.126 4.545 3.788 -2.504 -1.811 -2.028 0.9737794484 595 4.126 4.545 3.788 -2.505 -1.811 -2.028 0.9737794369 powell nthiter 6: fret = 0.973779 607 4.126 4.544 3.789 -2.505 -1.812 -2.029 0.9737793331 631 4.126 4.544 3.788 -2.505 -1.812 -2.029 0.9737792295 642 4.126 4.544 3.788 -2.511 -1.812 -2.029 0.9737791236 643 4.126 4.544 3.788 -2.508 -1.812 -2.029 0.9737775408 654 4.126 4.544 3.788 -2.508 -1.812 -2.027 0.9737770026 665 4.127 4.544 3.788 -2.508 -1.812 -2.027 0.9737769296 666 4.127 4.544 3.788 -2.508 -1.812 -2.027 0.9737769294 powell nthiter 7: fret = 0.973777 680 4.128 4.542 3.792 -2.508 -1.815 -2.029 0.9737752585 681 4.128 4.542 3.791 -2.508 -1.814 -2.028 0.9737750691 682 4.128 4.543 3.790 -2.508 -1.814 -2.028 0.9737750546 706 4.128 4.543 3.791 -2.508 -1.814 -2.028 0.9737748390 707 4.128 4.543 3.792 -2.508 -1.814 -2.028 0.9737748069 722 4.128 4.543 3.792 -2.510 -1.814 -2.028 0.9737745783 724 4.128 4.543 3.792 -2.509 -1.814 -2.028 0.9737744348 733 4.128 4.543 3.792 -2.509 -1.814 -2.027 0.9737742528 743 4.129 4.543 3.792 -2.509 -1.814 -2.027 0.9737739530 745 4.129 4.543 3.792 -2.509 -1.814 -2.027 0.9737739367 749 4.132 4.541 3.797 -2.510 -1.815 -2.027 0.9737724499 752 4.135 4.539 3.804 -2.512 -1.819 -2.027 0.9737720203 753 4.134 4.540 3.801 -2.512 -1.818 -2.027 0.9737715182 759 4.134 4.540 3.801 -2.512 -1.817 -2.027 0.9737715103 765 4.134 4.540 3.801 -2.512 -1.817 -2.027 0.9737715101 766 4.134 4.540 3.801 -2.512 -1.817 -2.027 0.9737714993 powell nthiter 8: fret = 0.973772 789 4.134 4.539 3.801 -2.512 -1.817 -2.027 0.9737712013 800 4.134 4.539 3.796 -2.512 -1.817 -2.027 0.9737706058 801 4.134 4.539 3.797 -2.512 -1.817 -2.027 0.9737701306 802 4.134 4.539 3.798 -2.512 -1.817 -2.027 0.9737699869 812 4.134 4.539 3.798 -2.533 -1.817 -2.027 0.9737660693 814 4.134 4.539 3.798 -2.529 -1.817 -2.027 0.9737657713 815 4.134 4.539 3.798 -2.528 -1.817 -2.027 0.9737655782 816 4.134 4.539 3.798 -2.522 -1.817 -2.027 0.9737651472 817 4.134 4.539 3.798 -2.524 -1.817 -2.027 0.9737650359 829 4.134 4.539 3.798 -2.524 -1.817 -2.023 0.9737629074 833 4.136 4.538 3.802 -2.525 -1.819 -2.023 0.9737579965 836 4.137 4.537 3.805 -2.526 -1.821 -2.023 0.9737569193 838 4.137 4.537 3.806 -2.526 -1.821 -2.023 0.9737568338 840 4.138 4.537 3.806 -2.526 -1.821 -2.023 0.9737568284 847 4.146 4.531 3.819 -2.542 -1.828 -2.019 0.9737532060 854 4.146 4.530 3.820 -2.543 -1.828 -2.018 0.9737530852 855 4.146 4.530 3.820 -2.543 -1.828 -2.018 0.9737530599 859 4.146 4.530 3.820 -2.543 -1.828 -2.018 0.9737530461 861 4.146 4.530 3.820 -2.543 -1.828 -2.018 0.9737530169 powell nthiter 9: fret = 0.973753 873 4.142 4.530 3.820 -2.544 -1.828 -2.019 0.9737523676 874 4.143 4.530 3.820 -2.544 -1.828 -2.019 0.9737519112 875 4.144 4.530 3.820 -2.544 -1.828 -2.019 0.9737517232 889 4.144 4.533 3.820 -2.544 -1.828 -2.019 0.9737505985 900 4.144 4.533 3.808 -2.544 -1.828 -2.019 0.9737478685 903 4.144 4.533 3.802 -2.544 -1.828 -2.019 0.9737444493 904 4.144 4.533 3.797 -2.544 -1.828 -2.019 0.9737443227 905 4.144 4.533 3.799 -2.544 -1.828 -2.019 0.9737437561 917 4.144 4.533 3.799 -2.545 -1.828 -2.019 0.9737432185 919 4.144 4.533 3.799 -2.547 -1.828 -2.019 0.9737429912 929 4.144 4.533 3.799 -2.547 -1.828 -2.016 0.9737393019 932 4.144 4.533 3.799 -2.547 -1.828 -2.012 0.9737370919 940 4.147 4.530 3.804 -2.553 -1.831 -2.011 0.9737318237 942 4.149 4.529 3.807 -2.557 -1.833 -2.010 0.9737315615 943 4.148 4.529 3.806 -2.555 -1.832 -2.010 0.9737311032 powell nthiter 10: fret = 0.973731 958 4.148 4.529 3.806 -2.555 -1.832 -2.010 0.9737309403 959 4.162 4.530 3.805 -2.553 -1.831 -2.010 0.9737280074 961 4.156 4.530 3.805 -2.554 -1.832 -2.010 0.9737253140 962 4.156 4.530 3.805 -2.554 -1.832 -2.010 0.9737252621 976 4.156 4.531 3.805 -2.554 -1.832 -2.010 0.9737249627 988 4.156 4.531 3.801 -2.554 -1.832 -2.010 0.9737219685 1012 4.156 4.531 3.801 -2.554 -1.832 -2.013 0.9737219189 1014 4.156 4.531 3.801 -2.554 -1.832 -2.012 0.9737218114 1021 4.157 4.530 3.802 -2.555 -1.832 -2.012 0.9737215131 1022 4.157 4.530 3.803 -2.556 -1.832 -2.011 0.9737214348 1023 4.157 4.530 3.802 -2.556 -1.832 -2.011 0.9737214067 powell nthiter 11: fret = 0.973721 1038 4.158 4.530 3.802 -2.556 -1.832 -2.011 0.9737213567 1040 4.158 4.530 3.802 -2.556 -1.832 -2.011 0.9737213513 1052 4.158 4.529 3.802 -2.556 -1.832 -2.011 0.9737211285 1063 4.158 4.529 3.801 -2.556 -1.832 -2.011 0.9737209562 1087 4.158 4.529 3.801 -2.556 -1.832 -2.012 0.9737208943 1094 4.158 4.529 3.801 -2.556 -1.832 -2.012 0.9737208682 1096 4.158 4.529 3.802 -2.557 -1.833 -2.012 0.9737207529 1098 4.158 4.528 3.803 -2.557 -1.833 -2.012 0.9737207017 1100 4.158 4.529 3.802 -2.557 -1.833 -2.012 0.9737206857 powell nthiter 12: fret = 0.973721 1113 4.158 4.529 3.802 -2.557 -1.833 -2.012 0.9737206840 1114 4.157 4.529 3.802 -2.557 -1.833 -2.012 0.9737206469 1116 4.157 4.529 3.802 -2.557 -1.833 -2.012 0.9737206362 1153 4.157 4.529 3.802 -2.556 -1.833 -2.012 0.9737205134 1165 4.157 4.529 3.802 -2.556 -1.833 -2.013 0.9737204607 1173 4.158 4.528 3.804 -2.557 -1.833 -2.013 0.9737203337 1179 4.158 4.528 3.804 -2.557 -1.833 -2.013 0.9737203225 powell nthiter 13: fret = 0.973720 1218 4.158 4.527 3.802 -2.557 -1.833 -2.013 0.9737201122 1252 4.158 4.527 3.803 -2.558 -1.834 -2.014 0.9737199657 1254 4.158 4.527 3.803 -2.559 -1.834 -2.013 0.9737198458 powell nthiter 14: fret = 0.973720 1267 4.158 4.527 3.803 -2.559 -1.834 -2.013 0.9737198392 Powell done niters = 14 Computing relative cost 0 -25.0 -25.0 -25.0 1.009574 1 -25.0 -25.0 25.0 1.033591 2 -25.0 25.0 -25.0 1.018845 3 -25.0 25.0 25.0 1.015683 4 25.0 -25.0 -25.0 1.038104 5 25.0 -25.0 25.0 1.048356 6 25.0 25.0 -25.0 1.022471 7 25.0 25.0 25.0 1.041853 REL: 8 0.973720 8.228477 1.028560 rel = 0.946683 Number of iterations 14 Min cost was 0.973720 Number of FunctionCalls 1334 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 67.618013 sec Parameters at optimum (transmm) 4.15814 4.52656 3.80323 Parameters at optimum (rotdeg) -2.55875 -1.83414 -2.01339 Final costs ---------------- Number of surface hits 253432 WM Intensity 293.6132 +/- 125.1986 Ctx Intensity 297.9291 +/- 124.8658 Pct Contrast 1.5292 +/- 42.5985 Cost 0.9737 RelCost 1.0184 Reg at min cost was -0.03510 0.99892 -0.03050 0.64652; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01603; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/002/register.dof6.dat, type = 14 Original Reg -0.06933 0.99759 0.00245 -3.76985; 0.99499 0.06932 -0.07208 4.04924; 0.07208 0.00256 0.99740 -3.49112; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.03423 -0.00133 0.03294 -4.41638; -0.00408 0.03503 -0.04565 -4.49252; 0.04672 -0.02883 -0.00179 -3.50715; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 7.928505 Computing change in rh position Surface-RMS-Diff-mm 8.010794 0.616584 9.713605 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done MinCost: 0.973720 293.613165 297.929114 1.529228 tkregister2_cmdl --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/002/template.nii.gz reg file bold/002/register.dof6.dat LoadVol 0 ZeroCRAS 0 7.4.1 Diagnostic Level -1 ---- Input registration matrix -------- -0.03510 0.99892 -0.03050 0.64652; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01603; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/002/template.nii.gz Tmov: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -88.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -0.03510 0.99892 -0.03050 0.64652; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01603; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = 20240801_dw204 RegMat --------------------------- -0.03510 0.99892 -0.03050 0.64652; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01603; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue Jun 17 12:53:55 EDT 2025 Ended at Tue Jun 17 12:55:49 EDT 2025 BBR-Run-Time-Sec 114 bbregister Done To check results, run: tkregisterfv --mov bold/002/template.nii.gz --reg bold/002/register.dof6.lta --surfs --sd /Volumes/umms-hillmera/asem_ptsd/DW204 Run: 003 ---------------- Tue Jun 17 12:55:50 EDT 2025 -------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 bbregister --s 20240801_dw204 --init-coreg --6 --bold --mov bold/003/template.nii.gz --reg bold/003/register.dof6.dat --lta bold/003/register.dof6.lta --init-reg-out bold/003/init.register.dof6.dat tmp bold/003/tmp.bbregister.90403 Log file is bold/003/register.dof6.log Tue Jun 17 12:55:50 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 /Applications/freesurfer/bin/bbregister --s 20240801_dw204 --init-coreg --6 --bold --mov bold/003/template.nii.gz --reg bold/003/register.dof6.dat --lta bold/003/register.dof6.lta --init-reg-out bold/003/init.register.dof6.dat FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 FREESURFER_HOME /Applications/freesurfer mri_convert bold/003/template.nii.gz bold/003/tmp.bbregister.90403/template.nii mri_convert bold/003/template.nii.gz bold/003/tmp.bbregister.90403/template.nii reading from bold/003/template.nii.gz... INFO: This is an unsigined short. TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) writing to bold/003/tmp.bbregister.90403/template.nii... mri_coreg --s 20240801_dw204 --mov bold/003/tmp.bbregister.90403/template.nii --regdat bold/003/tmp.bbregister.90403/reg.init.dat --reg bold/003/tmp.bbregister.90403/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 cmdline mri_coreg --s 20240801_dw204 --mov bold/003/tmp.bbregister.90403/template.nii --regdat bold/003/tmp.bbregister.90403/reg.init.dat --reg bold/003/tmp.bbregister.90403/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov bold/003/tmp.bbregister.90403/template.nii INFO: This is an unsigined short. Reading in ref /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/brainmask.mgz Reading in and applying refmask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz Setting cras translation parameters to align volume centers Init matrix params 1.2987 -13.9649 6.4966 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 -1.29869; 0.00000 1.00000 0.00000 13.96490; 0.00000 0.00000 1.00000 -6.49658; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt 1.2987 -13.9649 6.4966 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 5517.0000 mov gstd 1.6917 1.6917 1.6917 Smoothing mov refsat = 116.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0450690499 nhits = 93574 out of 16777216, Percent Overlap: 35.7 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 1.29869; 0.00000 1.00000 0.00000 -13.96490; 0.00000 0.00000 1.00000 6.49658; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.50000 0.00000 0.00000 -9.24999; 0.00000 0.18649 -0.46392 89.87160; 0.00000 -0.46392 -0.18649 114.42754; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 1.29869 0.03510 2.49658 0.00000 0.00000 0.00000 -1.0413554 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: 1.298691 0.035103 2.496582 0.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0648360252 #@# 4 188 1.29869 0.03510 2.49658 0.00000 0.00000 0.00000 -1.0648360 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.064836 #@# 4 191 -0.31934 0.03510 2.49658 0.00000 0.00000 0.00000 -1.0658149 #@# 4 192 -0.12098 0.03510 2.49658 0.00000 0.00000 0.00000 -1.0658928 #@# 4 195 0.08615 0.03510 2.49658 0.00000 0.00000 0.00000 -1.0658956 #@# 4 196 -0.00715 0.03510 2.49658 0.00000 0.00000 0.00000 -1.0659010 #@# 4 197 0.00285 0.03510 2.49658 0.00000 0.00000 0.00000 -1.0659016 #@# 4 198 0.01882 0.03510 2.49658 0.00000 0.00000 0.00000 -1.0659018 #@# 4 207 0.01882 -0.12966 2.49658 0.00000 0.00000 0.00000 -1.0659177 #@# 4 209 0.01882 -0.14313 2.49658 0.00000 0.00000 0.00000 -1.0659193 #@# 4 213 0.01882 -0.14313 0.87855 0.00000 0.00000 0.00000 -1.0660132 #@# 4 214 0.01882 -0.14313 1.60035 0.00000 0.00000 0.00000 -1.0661834 #@# 4 220 0.01882 -0.14313 1.64723 0.00000 0.00000 0.00000 -1.0661856 #@# 4 228 0.01882 -0.14313 1.64723 -0.61803 0.00000 0.00000 -1.0662184 #@# 4 230 0.01882 -0.14313 1.64723 -0.44037 0.00000 0.00000 -1.0662404 #@# 4 233 0.01882 -0.14313 1.64723 -0.45037 0.00000 0.00000 -1.0662425 #@# 4 234 0.01882 -0.14313 1.64723 -0.51441 0.00000 0.00000 -1.0662482 #@# 4 239 0.01882 -0.14313 1.64723 -0.51441 1.00000 0.00000 -1.0662941 #@# 4 243 0.01882 -0.14313 1.64723 -0.51441 0.61803 0.00000 -1.0663141 #@# 4 245 0.01882 -0.14313 1.64723 -0.51441 0.66713 0.00000 -1.0663199 #@# 4 247 0.01882 -0.14313 1.64723 -0.51441 0.68189 0.00000 -1.0663208 #@# 4 248 0.01882 -0.14313 1.64723 -0.51441 0.70341 0.00000 -1.0663223 #@# 4 258 0.01882 -0.14313 1.64723 -0.51441 0.70341 0.11755 -1.0663285 #@# 4 259 0.01882 -0.14313 1.64723 -0.51441 0.70341 0.12816 -1.0663311 powell nthiter 1: fret = -1.066331 #@# 4 270 -0.07112 -0.14313 1.64723 -0.51441 0.70341 0.12816 -1.0663352 #@# 4 271 -0.05275 -0.14313 1.64723 -0.51441 0.70341 0.12816 -1.0663377 #@# 4 280 -0.05275 -0.13127 1.64723 -0.51441 0.70341 0.12816 -1.0663383 #@# 4 283 -0.05275 -0.12127 1.64723 -0.51441 0.70341 0.12816 -1.0663387 #@# 4 292 -0.05275 -0.12127 1.38350 -0.51441 0.70341 0.12816 -1.0663484 #@# 4 295 -0.05275 -0.12127 1.32582 -0.51441 0.70341 0.12816 -1.0663511 #@# 4 304 -0.05275 -0.12127 1.32582 -0.66538 0.70341 0.12816 -1.0663573 Powell done niters total = 1 OptTimeSec 5.7 sec OptTimeMin 0.09 min nEvals 331 Final optimized parameters -0.05275460 -0.12126504 1.32581723 -0.66538060 0.70340550 0.12815760 Final matrix parameters -0.0528 -0.1213 1.3258 -0.6654 0.7034 0.1171 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.066357263444091 --------------------------------- Final RefRAS-to-MovRAS 0.99992 0.00224 0.01228 -0.05275; -0.00209 0.99993 -0.01161 -0.12127; -0.01230 0.01159 0.99986 1.32582; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.49996 0.00614 -0.00112 -9.25604; -0.00327 0.18108 -0.46605 85.73827; 0.00532 -0.46602 -0.18111 108.51768; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters -0.0528 -0.1213 1.3258 -0.6654 0.7034 0.1282 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters -0.0528 -0.1213 1.3258 -0.6654 0.7034 0.1282 nhits = 93037 out of 16777216, Percent Overlap: 35.5 mri_coreg RunTimeSec 30.6 sec To check run: tkregisterfv --mov bold/003/tmp.bbregister.90403/template.nii --targ /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/brainmask.mgz --reg bold/003/tmp.bbregister.90403/mri_coreg.lta --s 20240801_dw204 --surfs mri_coreg done mri_segreg --mov bold/003/tmp.bbregister.90403/template.nii --init-reg bold/003/tmp.bbregister.90403/reg.init.dat --out-reg bold/003/tmp.bbregister.90403/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 mri_segreg --mov bold/003/tmp.bbregister.90403/template.nii --init-reg bold/003/tmp.bbregister.90403/reg.init.dat --out-reg bold/003/tmp.bbregister.90403/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/003/tmp.bbregister.90403/template.nii regfile bold/003/tmp.bbregister.90403/reg.init.dat subject 20240801_dw204 dof 6 outregfile bold/003/tmp.bbregister.90403/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750594683 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99992 0.00224 0.01228 -0.76309; -0.01063 -0.36221 0.93204 -11.26732; -0.00653 0.93209 0.36216 12.31083; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.017655 1 -25.0 -25.0 25.0 1.001389 2 -25.0 25.0 -25.0 1.034561 3 -25.0 25.0 25.0 1.001483 4 25.0 -25.0 -25.0 1.045787 5 25.0 -25.0 25.0 0.986037 6 25.0 25.0 -25.0 0.974349 7 25.0 25.0 25.0 1.049051 REL: 8 0.909290 8.110312 1.013789 rel = 0.896923 Initial costs ---------------- Number of surface hits 2538 WM Intensity 1701.3534 +/- 574.5491 Ctx Intensity 1709.8666 +/- 584.5436 Pct Contrast 0.3882 +/- 20.8050 Cost 0.9093 RelCost 0.8969 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0188 1.0188 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0037 1.0037 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9758 0.9758 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9715 0.9715 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.9337 0.9337 0.0 121 -4.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.9290 0.9290 0.0 243 0.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9209 0.9209 0.0 246 0.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.9054 0.9054 0.0 255 0.0000 -4.0000 -4.0000 0.0000 0.0000 -4.0000 0.8981 0.8981 0.0 256 0.0000 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.8325 0.8325 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7559 0.7559 0.0 Brute Force -------------------------- Min cost was 0.755860 Number of iterations 729 Search time 0.843190 sec Parameters at best (transmm, rotdeg) 0.000 -4.000 0.000 -4.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -4 2 0 3 -4 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.755860 7 0.116 -4.000 0.000 -4.000 0.000 0.000 0.7539500790 8 0.148 -4.000 0.000 -4.000 0.000 0.000 0.7534737684 9 0.237 -4.000 0.000 -4.000 0.000 0.000 0.7529518426 12 0.258 -4.000 0.000 -4.000 0.000 0.000 0.7529315267 13 0.251 -4.000 0.000 -4.000 0.000 0.000 0.7529137604 23 0.251 -3.937 0.000 -4.000 0.000 0.000 0.7518341588 24 0.251 -3.815 0.000 -4.000 0.000 0.000 0.7508894638 26 0.251 -3.844 0.000 -4.000 0.000 0.000 0.7508093643 29 0.251 -3.857 0.000 -4.000 0.000 0.000 0.7508024709 30 0.251 -3.853 0.000 -4.000 0.000 0.000 0.7508006121 42 0.251 -3.852 -0.011 -4.000 0.000 0.000 0.7506825383 43 0.251 -3.852 -0.031 -4.000 0.000 0.000 0.7505786579 45 0.251 -3.852 -0.029 -4.000 0.000 0.000 0.7505754215 48 0.251 -3.852 -0.028 -4.000 0.000 0.000 0.7505746350 51 0.251 -3.852 -0.028 -3.000 0.000 0.000 0.7472789975 52 0.251 -3.852 -0.028 -1.382 0.000 0.000 0.7330358165 57 0.251 -3.852 -0.028 -1.494 0.000 0.000 0.7314057674 58 0.251 -3.852 -0.028 -1.577 0.000 0.000 0.7300102009 60 0.251 -3.852 -0.028 -1.609 0.000 0.000 0.7299691551 61 0.251 -3.852 -0.028 -1.598 0.000 0.000 0.7299384357 62 0.251 -3.852 -0.028 -1.596 0.000 0.000 0.7299380477 63 0.251 -3.852 -0.028 -1.595 0.000 0.000 0.7299380375 69 0.251 -3.852 -0.028 -1.595 -0.618 0.000 0.7207300004 70 0.251 -3.852 -0.028 -1.595 -1.000 0.000 0.7178122246 72 0.251 -3.852 -0.028 -1.595 -0.908 0.000 0.7161062380 73 0.251 -3.852 -0.028 -1.595 -0.851 0.000 0.7158088422 75 0.251 -3.852 -0.028 -1.595 -0.861 0.000 0.7158029752 77 0.251 -3.852 -0.028 -1.595 -0.858 0.000 0.7158007269 78 0.251 -3.852 -0.028 -1.595 -0.857 0.000 0.7158005315 84 0.251 -3.852 -0.028 -1.595 -0.857 -0.618 0.7069395116 86 0.251 -3.852 -0.028 -1.595 -0.857 -0.510 0.7065840551 88 0.251 -3.852 -0.028 -1.595 -0.857 -0.474 0.7065412758 93 0.251 -3.852 -0.028 -1.595 -0.857 -0.476 0.7065405546 powell nthiter 1: fret = 0.706541 107 0.258 -3.852 -0.028 -1.595 -0.857 -0.476 0.7065308012 108 0.257 -3.852 -0.028 -1.595 -0.857 -0.476 0.7065305802 122 0.257 -3.854 -0.028 -1.595 -0.857 -0.476 0.7065289873 127 0.257 -3.854 -1.646 -1.595 -0.857 -0.476 0.7005286153 128 0.257 -3.854 -0.909 -1.595 -0.857 -0.476 0.6987892787 130 0.257 -3.854 -0.572 -1.595 -0.857 -0.476 0.6975048840 132 0.257 -3.854 -0.676 -1.595 -0.857 -0.476 0.6972398644 133 0.257 -3.854 -0.671 -1.595 -0.857 -0.476 0.6972039809 134 0.257 -3.854 -0.638 -1.595 -0.857 -0.476 0.6971786999 136 0.257 -3.854 -0.652 -1.595 -0.857 -0.476 0.6971490556 144 0.257 -3.854 -0.652 -1.214 -0.857 -0.476 0.6928173676 146 0.257 -3.854 -0.652 -1.344 -0.857 -0.476 0.6897177813 159 0.257 -3.854 -0.652 -1.344 -0.842 -0.476 0.6896747029 169 0.257 -3.854 -0.652 -1.344 -0.842 -0.406 0.6896302914 171 0.257 -3.854 -0.652 -1.344 -0.842 -0.438 0.6895606213 174 0.257 -3.854 -0.652 -1.344 -0.842 -0.444 0.6895561305 powell nthiter 2: fret = 0.689556 184 0.338 -3.854 -0.652 -1.344 -0.842 -0.444 0.6888620270 186 0.311 -3.854 -0.652 -1.344 -0.842 -0.444 0.6886268763 188 0.310 -3.854 -0.652 -1.344 -0.842 -0.444 0.6886266952 195 0.310 -3.472 -0.652 -1.344 -0.842 -0.444 0.6881149148 197 0.310 -3.236 -0.652 -1.344 -0.842 -0.444 0.6837291399 199 0.310 -3.269 -0.652 -1.344 -0.842 -0.444 0.6834568347 201 0.310 -3.274 -0.652 -1.344 -0.842 -0.444 0.6834402489 202 0.310 -3.277 -0.652 -1.344 -0.842 -0.444 0.6834310931 205 0.310 -3.278 -0.652 -1.344 -0.842 -0.444 0.6834310578 211 0.310 -3.278 -1.270 -1.344 -0.842 -0.444 0.6747911441 213 0.310 -3.278 -1.301 -1.344 -0.842 -0.444 0.6746110166 215 0.310 -3.278 -1.309 -1.344 -0.842 -0.444 0.6746027001 216 0.310 -3.278 -1.310 -1.344 -0.842 -0.444 0.6746023959 217 0.310 -3.278 -1.311 -1.344 -0.842 -0.444 0.6746020394 221 0.310 -3.278 -1.314 -1.344 -0.842 -0.444 0.6746019217 223 0.310 -3.278 -1.313 -1.344 -0.842 -0.444 0.6746019106 229 0.310 -3.278 -1.313 -0.962 -0.842 -0.444 0.6705844081 230 0.310 -3.278 -1.313 -0.990 -0.842 -0.444 0.6704686233 233 0.310 -3.278 -1.313 -0.988 -0.842 -0.444 0.6704676791 243 0.310 -3.278 -1.313 -0.988 -0.460 -0.444 0.6673696523 244 0.310 -3.278 -1.313 -0.988 -0.544 -0.444 0.6654742584 245 0.310 -3.278 -1.313 -0.988 -0.611 -0.444 0.6651436204 246 0.310 -3.278 -1.313 -0.988 -0.599 -0.444 0.6651344821 247 0.310 -3.278 -1.313 -0.988 -0.601 -0.444 0.6651273484 248 0.310 -3.278 -1.313 -0.988 -0.604 -0.444 0.6651254800 249 0.310 -3.278 -1.313 -0.988 -0.603 -0.444 0.6651254407 255 0.310 -3.278 -1.313 -0.988 -0.603 -0.062 0.6606364356 256 0.310 -3.278 -1.313 -0.988 -0.603 -0.129 0.6598173138 257 0.310 -3.278 -1.313 -0.988 -0.603 -0.176 0.6597062990 259 0.310 -3.278 -1.313 -0.988 -0.603 -0.182 0.6597061175 260 0.310 -3.278 -1.313 -0.988 -0.603 -0.179 0.6597053325 powell nthiter 3: fret = 0.659705 272 0.263 -3.278 -1.313 -0.988 -0.603 -0.180 0.6594025989 273 0.254 -3.278 -1.313 -0.988 -0.603 -0.180 0.6593895291 274 0.250 -3.278 -1.313 -0.988 -0.603 -0.180 0.6593859526 278 0.251 -3.278 -1.313 -0.988 -0.603 -0.180 0.6593852399 286 0.251 -3.264 -1.313 -0.988 -0.603 -0.180 0.6587436414 287 0.251 -3.157 -1.313 -0.988 -0.603 -0.180 0.6581421654 289 0.251 -3.202 -1.313 -0.988 -0.603 -0.180 0.6574928545 291 0.251 -3.209 -1.313 -0.988 -0.603 -0.180 0.6574928398 293 0.251 -3.205 -1.313 -0.988 -0.603 -0.180 0.6574875381 302 0.251 -3.205 -1.477 -0.988 -0.603 -0.180 0.6565308682 303 0.251 -3.205 -1.450 -0.988 -0.603 -0.180 0.6564430157 307 0.251 -3.205 -1.449 -0.988 -0.603 -0.180 0.6564418802 314 0.251 -3.205 -1.449 -0.935 -0.603 -0.180 0.6564294784 315 0.251 -3.205 -1.449 -0.957 -0.603 -0.180 0.6563306819 316 0.251 -3.205 -1.449 -0.960 -0.603 -0.180 0.6563291088 318 0.251 -3.205 -1.449 -0.959 -0.603 -0.180 0.6563288621 326 0.251 -3.205 -1.449 -0.959 -0.571 -0.180 0.6562063705 328 0.251 -3.205 -1.449 -0.959 -0.580 -0.180 0.6561782399 329 0.251 -3.205 -1.449 -0.959 -0.583 -0.180 0.6561765821 330 0.251 -3.205 -1.449 -0.959 -0.582 -0.180 0.6561761215 338 0.251 -3.205 -1.449 -0.959 -0.582 -0.127 0.6559622459 340 0.251 -3.205 -1.449 -0.959 -0.582 -0.139 0.6559208105 powell nthiter 4: fret = 0.655921 355 0.253 -3.205 -1.449 -0.959 -0.582 -0.139 0.6559182342 356 0.254 -3.205 -1.449 -0.959 -0.582 -0.139 0.6559162775 357 0.257 -3.205 -1.449 -0.959 -0.582 -0.139 0.6559150123 359 0.256 -3.205 -1.449 -0.959 -0.582 -0.139 0.6559146612 368 0.256 -3.213 -1.449 -0.959 -0.582 -0.139 0.6558916252 369 0.256 -3.215 -1.449 -0.959 -0.582 -0.139 0.6558909725 377 0.256 -3.215 -1.487 -0.959 -0.582 -0.139 0.6557202648 393 0.256 -3.215 -1.487 -0.966 -0.582 -0.139 0.6557175881 394 0.256 -3.215 -1.487 -0.965 -0.582 -0.139 0.6557167831 404 0.256 -3.215 -1.487 -0.965 -0.584 -0.139 0.6557102171 407 0.256 -3.215 -1.487 -0.965 -0.585 -0.139 0.6557100712 417 0.256 -3.215 -1.487 -0.965 -0.585 -0.138 0.6557080715 418 0.256 -3.215 -1.487 -0.965 -0.585 -0.136 0.6557065659 powell nthiter 5: fret = 0.655707 431 0.269 -3.215 -1.487 -0.965 -0.585 -0.136 0.6556756354 432 0.266 -3.215 -1.487 -0.965 -0.585 -0.136 0.6556715763 443 0.266 -3.221 -1.487 -0.965 -0.585 -0.136 0.6556596557 444 0.266 -3.220 -1.487 -0.965 -0.585 -0.136 0.6556596437 452 0.266 -3.220 -1.492 -0.965 -0.585 -0.136 0.6556563423 453 0.266 -3.220 -1.495 -0.965 -0.585 -0.136 0.6556563167 467 0.266 -3.220 -1.494 -0.974 -0.585 -0.136 0.6556437591 469 0.266 -3.220 -1.494 -0.975 -0.585 -0.136 0.6556435115 470 0.266 -3.220 -1.494 -0.976 -0.585 -0.136 0.6556434246 480 0.266 -3.220 -1.494 -0.976 -0.586 -0.136 0.6556433309 490 0.266 -3.220 -1.494 -0.976 -0.586 -0.135 0.6556410793 491 0.266 -3.220 -1.494 -0.976 -0.586 -0.131 0.6556361697 493 0.266 -3.220 -1.494 -0.976 -0.586 -0.129 0.6556359804 495 0.266 -3.220 -1.494 -0.976 -0.586 -0.130 0.6556354118 powell nthiter 6: fret = 0.655635 507 0.273 -3.220 -1.494 -0.976 -0.586 -0.130 0.6556209012 508 0.272 -3.220 -1.494 -0.976 -0.586 -0.130 0.6556204169 518 0.272 -3.221 -1.494 -0.976 -0.586 -0.130 0.6556180183 526 0.272 -3.221 -1.490 -0.976 -0.586 -0.130 0.6556159678 529 0.272 -3.221 -1.488 -0.976 -0.586 -0.130 0.6556157685 541 0.272 -3.221 -1.488 -0.979 -0.586 -0.130 0.6556115299 543 0.272 -3.221 -1.488 -0.981 -0.586 -0.130 0.6556113219 545 0.272 -3.221 -1.488 -0.980 -0.586 -0.130 0.6556104374 554 0.272 -3.221 -1.488 -0.980 -0.587 -0.130 0.6556068788 556 0.272 -3.221 -1.488 -0.980 -0.591 -0.130 0.6556045090 557 0.272 -3.221 -1.488 -0.980 -0.590 -0.130 0.6556037193 568 0.272 -3.221 -1.488 -0.980 -0.590 -0.129 0.6556035008 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 0.979586 1 -25.0 -25.0 25.0 1.008837 2 -25.0 25.0 -25.0 1.009949 3 -25.0 25.0 25.0 0.971834 4 25.0 -25.0 -25.0 1.013372 5 25.0 -25.0 25.0 1.012041 6 25.0 25.0 -25.0 0.989947 7 25.0 25.0 25.0 0.993784 REL: 8 0.655604 7.979349 0.997419 rel = 0.6573 Number of iterations 6 Min cost was 0.655604 Number of FunctionCalls 570 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.669019 sec Parameters at optimum (transmm) 0.27162 -3.22146 -1.48833 Parameters at optimum (rotdeg) -0.98011 -0.58987 -0.12875 Final costs ---------------- Number of surface hits 2538 WM Intensity 1617.8703 +/- 570.5129 Ctx Intensity 1719.5318 +/- 598.7997 Pct Contrast 5.7644 +/- 20.9408 Cost 0.6556 RelCost 0.8969 Reg at min cost was 0.99991 -0.00820 0.01082 -0.64498; -0.01299 -0.34620 0.93807 -14.27451; 0.00395 0.93813 0.34627 11.00491; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/003/tmp.bbregister.90403/bbr.pass1.dat, type = 14 Original Reg 0.99992 0.00224 0.01228 -0.76309; -0.01063 -0.36221 0.93204 -11.26732; -0.00653 0.93209 0.36216 12.31083; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00001 0.01044 0.00146 -0.11811; 0.00236 -0.01601 -0.00604 3.00719; -0.01048 -0.00603 0.01589 1.30592; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 3.823759 Computing change in rh position Surface-RMS-Diff-mm 3.731986 0.685374 5.037758 mri_segreg done mri_segreg --mov bold/003/tmp.bbregister.90403/template.nii --init-reg bold/003/tmp.bbregister.90403/bbr.pass1.dat --out-reg bold/003/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/003/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/003/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/003/tmp.bbregister.90403/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 mri_segreg --mov bold/003/tmp.bbregister.90403/template.nii --init-reg bold/003/tmp.bbregister.90403/bbr.pass1.dat --out-reg bold/003/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/003/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/003/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/003/tmp.bbregister.90403/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/003/tmp.bbregister.90403/template.nii regfile bold/003/tmp.bbregister.90403/bbr.pass1.dat subject 20240801_dw204 dof 6 outregfile bold/003/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750297451 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99991 -0.00820 0.01082 -0.64498; -0.01299 -0.34620 0.93807 -14.27451; 0.00395 0.93813 0.34627 11.00491; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.995689 1 -25.0 -25.0 25.0 0.995347 2 -25.0 25.0 -25.0 0.997625 3 -25.0 25.0 25.0 0.991050 4 25.0 -25.0 -25.0 1.015710 5 25.0 -25.0 25.0 0.997713 6 25.0 25.0 -25.0 0.988852 7 25.0 25.0 25.0 1.002274 REL: 8 0.677978 7.984261 0.998033 rel = 0.679315 Initial costs ---------------- Number of surface hits 253432 WM Intensity 1619.3347 +/- 572.4375 Ctx Intensity 1724.6172 +/- 595.7446 Pct Contrast 6.0811 +/- 20.5822 Cost 0.6780 RelCost 0.6793 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.6686 0.6686 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.6669 0.6669 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.6659 0.6659 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.6647 0.6647 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.6633 0.6633 0.0 15 -0.1000 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.6629 0.6629 0.0 33 -0.1000 -0.1000 0.0000 -0.1000 0.1000 -0.1000 0.6627 0.6627 0.0 86 -0.1000 0.0000 -0.1000 -0.1000 0.0000 0.1000 0.6623 0.6623 0.0 94 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.6616 0.6616 0.0 95 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.1000 0.6612 0.6612 0.0 118 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0000 0.6606 0.6606 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.6595 0.6595 0.0 148 -0.1000 0.0000 0.1000 0.0000 0.0000 0.0000 0.6594 0.6594 0.0 210 -0.1000 0.1000 0.0000 0.1000 0.0000 -0.1000 0.6593 0.6593 0.0 255 0.0000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.6587 0.6587 0.0 256 0.0000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.6585 0.6585 0.0 264 0.0000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.6579 0.6579 0.0 265 0.0000 -0.1000 -0.1000 0.1000 0.0000 0.0000 0.6576 0.6576 0.0 292 0.0000 -0.1000 0.0000 0.1000 0.0000 0.0000 0.6575 0.6575 0.0 337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.6571 0.6571 0.0 346 0.0000 0.0000 -0.1000 0.1000 0.0000 0.0000 0.6565 0.6565 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.6556 0.6556 0.0 592 0.1000 0.0000 -0.1000 0.1000 0.1000 0.0000 0.6553 0.6553 0.0 Brute Force -------------------------- Min cost was 0.655327 Number of iterations 729 Search time 0.650214 sec Parameters at best (transmm, rotdeg) 0.100 0.000 -0.100 0.100 0.100 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0.1 1 0 2 -0.1 3 0.1 4 0.1 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.676394 8 0.119 0.000 -0.100 0.100 0.100 0.000 0.6763730713 10 0.118 0.000 -0.100 0.100 0.100 0.000 0.6763729132 12 0.117 0.000 -0.100 0.100 0.100 0.000 0.6763727881 21 0.116 0.095 -0.100 0.100 0.100 0.000 0.6761578437 22 0.116 0.093 -0.100 0.100 0.100 0.000 0.6761563971 23 0.116 0.083 -0.100 0.100 0.100 0.000 0.6761528200 25 0.116 0.085 -0.100 0.100 0.100 0.000 0.6761526958 33 0.116 0.085 0.282 0.100 0.100 0.000 0.6741150598 34 0.116 0.085 0.169 0.100 0.100 0.000 0.6735657779 35 0.116 0.085 0.161 0.100 0.100 0.000 0.6735655345 36 0.116 0.085 0.165 0.100 0.100 0.000 0.6735648566 37 0.116 0.085 0.166 0.100 0.100 0.000 0.6735648458 44 0.116 0.085 0.166 0.482 0.100 0.000 0.6729476752 45 0.116 0.085 0.166 0.343 0.100 0.000 0.6727353674 46 0.116 0.085 0.166 0.353 0.100 0.000 0.6727202714 47 0.116 0.085 0.166 0.380 0.100 0.000 0.6727108911 49 0.116 0.085 0.166 0.372 0.100 0.000 0.6727092609 52 0.116 0.085 0.166 0.370 0.100 0.000 0.6727090992 61 0.116 0.085 0.166 0.370 0.208 0.000 0.6722708872 62 0.116 0.085 0.166 0.370 0.205 0.000 0.6722683338 63 0.116 0.085 0.166 0.370 0.198 0.000 0.6722652686 65 0.116 0.085 0.166 0.370 0.195 0.000 0.6722649958 74 0.116 0.085 0.166 0.370 0.195 0.166 0.6717743687 75 0.116 0.085 0.166 0.370 0.195 0.167 0.6717737839 76 0.116 0.085 0.166 0.370 0.195 0.187 0.6717642248 80 0.116 0.085 0.166 0.370 0.195 0.192 0.6717637706 82 0.116 0.085 0.166 0.370 0.195 0.191 0.6717637215 powell nthiter 1: fret = 0.671764 93 0.117 0.085 0.166 0.370 0.195 0.191 0.6717636518 101 0.118 0.141 0.166 0.370 0.195 0.191 0.6715866064 102 0.118 0.163 0.166 0.370 0.195 0.191 0.6715713075 103 0.118 0.164 0.166 0.370 0.195 0.191 0.6715710285 104 0.118 0.172 0.166 0.370 0.195 0.191 0.6715708084 106 0.118 0.169 0.166 0.370 0.195 0.191 0.6715700958 115 0.118 0.168 0.053 0.370 0.195 0.191 0.6709626617 117 0.118 0.168 0.057 0.370 0.195 0.191 0.6709620764 126 0.118 0.168 0.056 0.473 0.195 0.191 0.6706654661 128 0.118 0.168 0.056 0.465 0.195 0.191 0.6706643987 129 0.118 0.168 0.056 0.467 0.195 0.191 0.6706641930 137 0.118 0.168 0.056 0.467 0.230 0.191 0.6705668786 138 0.118 0.168 0.056 0.467 0.243 0.191 0.6705557680 139 0.118 0.168 0.056 0.467 0.246 0.191 0.6705553125 powell nthiter 2: fret = 0.670555 158 0.102 0.168 0.056 0.467 0.246 0.191 0.6705201405 159 0.092 0.168 0.056 0.467 0.246 0.191 0.6705149108 160 0.093 0.168 0.056 0.467 0.246 0.191 0.6705148387 168 0.093 0.196 0.056 0.467 0.246 0.191 0.6704977713 169 0.093 0.193 0.056 0.467 0.246 0.191 0.6704968747 170 0.093 0.190 0.056 0.467 0.246 0.191 0.6704968403 172 0.093 0.191 0.056 0.467 0.246 0.191 0.6704967180 180 0.093 0.191 0.015 0.467 0.246 0.191 0.6704587457 181 0.093 0.191 0.024 0.467 0.246 0.191 0.6704551105 191 0.093 0.191 0.023 0.484 0.246 0.191 0.6704397268 192 0.093 0.191 0.023 0.489 0.246 0.191 0.6704391143 193 0.093 0.191 0.023 0.488 0.246 0.191 0.6704390943 202 0.093 0.191 0.023 0.488 0.245 0.191 0.6704390892 211 0.093 0.191 0.023 0.488 0.245 0.190 0.6704390014 212 0.093 0.191 0.023 0.488 0.245 0.189 0.6704389937 powell nthiter 3: fret = 0.670439 225 0.086 0.191 0.023 0.488 0.245 0.188 0.6704360068 227 0.087 0.191 0.023 0.488 0.245 0.188 0.6704359855 246 0.087 0.191 0.018 0.488 0.245 0.188 0.6704348918 267 0.087 0.191 0.017 0.488 0.247 0.188 0.6704347558 278 0.087 0.191 0.017 0.488 0.248 0.189 0.6704347474 powell nthiter 4: fret = 0.670435 288 0.088 0.191 0.017 0.488 0.248 0.189 0.6704347303 318 0.088 0.191 0.017 0.489 0.248 0.189 0.6704345403 337 0.088 0.191 0.017 0.489 0.247 0.190 0.6704345137 powell nthiter 5: fret = 0.670435 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 0.997516 1 -25.0 -25.0 25.0 0.997501 2 -25.0 25.0 -25.0 0.999672 3 -25.0 25.0 25.0 0.993644 4 25.0 -25.0 -25.0 1.017266 5 25.0 -25.0 25.0 0.995198 6 25.0 25.0 -25.0 0.989042 7 25.0 25.0 25.0 1.004618 REL: 8 0.670435 7.994458 0.999307 rel = 0.670899 Number of iterations 5 Min cost was 0.670435 Number of FunctionCalls 400 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 18.672300 sec Parameters at optimum (transmm) 0.08665 0.19209 0.01700 Parameters at optimum (rotdeg) 0.48940 0.24671 0.18980 Final costs ---------------- Number of surface hits 253432 WM Intensity 1623.3550 +/- 573.8335 Ctx Intensity 1734.0300 +/- 598.4866 Pct Contrast 6.3973 +/- 20.4376 Cost 0.6704 RelCost 0.6793 Reg at min cost was 0.99995 -0.00300 0.00925 -0.46386; -0.00971 -0.35421 0.93512 -14.17781; -0.00047 0.93516 0.35422 10.90226; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/003/register.dof6.dat, type = 14 Original Reg 0.99991 -0.00820 0.01082 -0.64498; -0.01299 -0.34620 0.93807 -14.27451; 0.00395 0.93813 0.34627 11.00491; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00004 -0.00520 0.00157 -0.18112; -0.00328 0.00801 0.00296 -0.09671; 0.00442 0.00296 -0.00795 0.10265; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.470481 Computing change in rh position Surface-RMS-Diff-mm 0.500360 0.188754 1.005669 mri_segreg done MinCost: 0.670435 1623.355038 1734.029951 6.397278 tkregister2_cmdl --mov bold/003/template.nii.gz --reg bold/003/register.dof6.dat --noedit --ltaout bold/003/register.dof6.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/003/template.nii.gz reg file bold/003/register.dof6.dat LoadVol 0 ZeroCRAS 0 7.4.1 Diagnostic Level -1 ---- Input registration matrix -------- 0.99995 -0.00300 0.00925 -0.46386; -0.00971 -0.35421 0.93512 -14.17781; -0.00047 0.93516 0.35422 10.90226; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: This is an unsigined short. INFO: loading target /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/003/template.nii.gz INFO: This is an unsigined short. Tmov: -------------------- -2.00000 0.00000 0.00000 110.00000; 0.00000 0.00000 2.00000 -64.00000; 0.00000 -2.00000 0.00000 110.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99995 -0.00300 0.00925 -0.46386; -0.00971 -0.35421 0.93512 -14.17781; -0.00047 0.93516 0.35422 10.90226; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = 20240801_dw204 RegMat --------------------------- 0.99995 -0.00300 0.00925 -0.46386; -0.00971 -0.35421 0.93512 -14.17781; -0.00047 0.93516 0.35422 10.90226; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue Jun 17 12:55:50 EDT 2025 Ended at Tue Jun 17 12:56:47 EDT 2025 BBR-Run-Time-Sec 57 bbregister Done To check results, run: tkregisterfv --mov bold/003/template.nii.gz --reg bold/003/register.dof6.lta --surfs --sd /Volumes/umms-hillmera/asem_ptsd/DW204 Run: 004 ---------------- Tue Jun 17 12:56:48 EDT 2025 -------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 bbregister --s 20240801_dw204 --init-coreg --6 --bold --mov bold/004/template.nii.gz --reg bold/004/register.dof6.dat --lta bold/004/register.dof6.lta --init-reg-out bold/004/init.register.dof6.dat tmp bold/004/tmp.bbregister.90505 Log file is bold/004/register.dof6.log Tue Jun 17 12:56:48 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 /Applications/freesurfer/bin/bbregister --s 20240801_dw204 --init-coreg --6 --bold --mov bold/004/template.nii.gz --reg bold/004/register.dof6.dat --lta bold/004/register.dof6.lta --init-reg-out bold/004/init.register.dof6.dat FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 FREESURFER_HOME /Applications/freesurfer mri_convert bold/004/template.nii.gz bold/004/tmp.bbregister.90505/template.nii mri_convert bold/004/template.nii.gz bold/004/tmp.bbregister.90505/template.nii reading from bold/004/template.nii.gz... INFO: This is an unsigined short. TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) writing to bold/004/tmp.bbregister.90505/template.nii... mri_coreg --s 20240801_dw204 --mov bold/004/tmp.bbregister.90505/template.nii --regdat bold/004/tmp.bbregister.90505/reg.init.dat --reg bold/004/tmp.bbregister.90505/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 cmdline mri_coreg --s 20240801_dw204 --mov bold/004/tmp.bbregister.90505/template.nii --regdat bold/004/tmp.bbregister.90505/reg.init.dat --reg bold/004/tmp.bbregister.90505/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov bold/004/tmp.bbregister.90505/template.nii INFO: This is an unsigined short. Reading in ref /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/brainmask.mgz Reading in and applying refmask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz Setting cras translation parameters to align volume centers Init matrix params 1.2987 -13.9649 6.4966 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 -1.29869; 0.00000 1.00000 0.00000 13.96490; 0.00000 0.00000 1.00000 -6.49658; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt 1.2987 -13.9649 6.4966 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 5364.6665 mov gstd 1.6917 1.6917 1.6917 Smoothing mov refsat = 116.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0451377161 nhits = 93574 out of 16777216, Percent Overlap: 35.7 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 1.29869; 0.00000 1.00000 0.00000 -13.96490; 0.00000 0.00000 1.00000 6.49658; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.50000 0.00000 0.00000 -9.24999; 0.00000 0.18649 -0.46392 89.87160; 0.00000 -0.46392 -0.18649 114.42754; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 1.29869 0.03510 2.49658 2.00000 0.00000 0.00000 -1.0419443 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: 1.298691 0.035103 2.496582 2.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0662406683 #@# 4 188 1.29869 0.03510 2.49658 2.00000 0.00000 0.00000 -1.0662407 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.066241 #@# 4 191 -0.31934 0.03510 2.49658 2.00000 0.00000 0.00000 -1.0671613 #@# 4 192 -0.00906 0.03510 2.49658 2.00000 0.00000 0.00000 -1.0672883 #@# 4 195 0.18174 0.03510 2.49658 2.00000 0.00000 0.00000 -1.0672959 #@# 4 196 0.10904 0.03510 2.49658 2.00000 0.00000 0.00000 -1.0673000 #@# 4 206 0.10904 -0.20603 2.49658 2.00000 0.00000 0.00000 -1.0673175 #@# 4 209 0.10904 -0.24878 2.49658 2.00000 0.00000 0.00000 -1.0673178 #@# 4 219 0.10904 -0.24878 2.31295 2.00000 0.00000 0.00000 -1.0673357 #@# 4 220 0.10904 -0.24878 2.30052 2.00000 0.00000 0.00000 -1.0673363 #@# 4 223 0.10904 -0.24878 2.29052 2.00000 0.00000 0.00000 -1.0673367 #@# 4 227 0.10904 -0.24878 2.29052 0.38197 0.00000 0.00000 -1.0673897 #@# 4 228 0.10904 -0.24878 2.29052 1.12061 0.00000 0.00000 -1.0675126 #@# 4 232 0.10904 -0.24878 2.29052 1.10097 0.00000 0.00000 -1.0675144 #@# 4 233 0.10904 -0.24878 2.29052 1.03190 0.00000 0.00000 -1.0675204 #@# 4 237 0.10904 -0.24878 2.29052 1.02190 0.00000 0.00000 -1.0675209 #@# 4 239 0.10904 -0.24878 2.29052 1.02190 1.00000 0.00000 -1.0676043 #@# 4 243 0.10904 -0.24878 2.29052 1.02190 0.61803 0.00000 -1.0676093 #@# 4 244 0.10904 -0.24878 2.29052 1.02190 0.74292 0.00000 -1.0676191 #@# 4 245 0.10904 -0.24878 2.29052 1.02190 0.79058 0.00000 -1.0676197 #@# 4 248 0.10904 -0.24878 2.29052 1.02190 0.82113 0.00000 -1.0676203 #@# 4 257 0.10904 -0.24878 2.29052 1.02190 0.82113 -0.12231 -1.0676223 #@# 4 258 0.10904 -0.24878 2.29052 1.02190 0.82113 -0.09377 -1.0676225 #@# 4 260 0.10904 -0.24878 2.29052 1.02190 0.82113 -0.10377 -1.0676227 powell nthiter 1: fret = -1.067623 #@# 4 268 0.03306 -0.24878 2.29052 1.02190 0.82113 -0.10377 -1.0676290 #@# 4 271 0.04306 -0.24878 2.29052 1.02190 0.82113 -0.10377 -1.0676298 #@# 4 278 0.04306 -0.17163 2.29052 1.02190 0.82113 -0.10377 -1.0676311 #@# 4 282 0.04306 -0.15244 2.29052 1.02190 0.82113 -0.10377 -1.0676323 #@# 4 288 0.04306 -0.15244 1.67248 1.02190 0.82113 -0.10377 -1.0676712 #@# 4 290 0.04306 -0.15244 1.90773 1.02190 0.82113 -0.10377 -1.0676903 #@# 4 301 0.04306 -0.15244 1.90773 0.88461 0.82113 -0.10377 -1.0676980 #@# 4 303 0.04306 -0.15244 1.90773 0.91932 0.82113 -0.10377 -1.0676985 Powell done niters total = 1 OptTimeSec 5.6 sec OptTimeMin 0.09 min nEvals 329 Final optimized parameters 0.04305677 -0.15243721 1.90772521 0.91931617 0.82113314 -0.10376538 Final matrix parameters 0.0431 -0.1524 1.9077 0.9193 0.8211 -0.0894 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.067698461110209 --------------------------------- Final RefRAS-to-MovRAS 0.99990 -0.00181 0.01433 0.04306; 0.00158 0.99987 0.01604 -0.15244; -0.01436 -0.01602 0.99977 1.90773; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.49995 0.00717 0.00091 -9.63271; -0.00194 0.19389 -0.46087 83.31055; 0.00696 -0.46082 -0.19390 109.15822; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters 0.0431 -0.1524 1.9077 0.9193 0.8211 -0.1038 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters 0.0431 -0.1524 1.9077 0.9193 0.8211 -0.1038 nhits = 92984 out of 16777216, Percent Overlap: 35.5 mri_coreg RunTimeSec 30.4 sec To check run: tkregisterfv --mov bold/004/tmp.bbregister.90505/template.nii --targ /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/brainmask.mgz --reg bold/004/tmp.bbregister.90505/mri_coreg.lta --s 20240801_dw204 --surfs mri_coreg done mri_segreg --mov bold/004/tmp.bbregister.90505/template.nii --init-reg bold/004/tmp.bbregister.90505/reg.init.dat --out-reg bold/004/tmp.bbregister.90505/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 mri_segreg --mov bold/004/tmp.bbregister.90505/template.nii --init-reg bold/004/tmp.bbregister.90505/reg.init.dat --out-reg bold/004/tmp.bbregister.90505/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/004/tmp.bbregister.90505/template.nii regfile bold/004/tmp.bbregister.90505/reg.init.dat subject 20240801_dw204 dof 6 outregfile bold/004/tmp.bbregister.90505/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750313171 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99990 -0.00181 0.01433 -0.78740; -0.01391 -0.38780 0.92164 -11.51114; -0.00389 0.92174 0.38779 12.22284; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.023923 1 -25.0 -25.0 25.0 0.989156 2 -25.0 25.0 -25.0 1.054533 3 -25.0 25.0 25.0 0.988953 4 25.0 -25.0 -25.0 1.029554 5 25.0 -25.0 25.0 0.993665 6 25.0 25.0 -25.0 1.008606 7 25.0 25.0 25.0 1.002543 REL: 8 0.877478 8.090933 1.011367 rel = 0.867616 Initial costs ---------------- Number of surface hits 2538 WM Intensity 1726.4080 +/- 556.0669 Ctx Intensity 1737.9852 +/- 568.2450 Pct Contrast 0.5293 +/- 22.9847 Cost 0.8775 RelCost 0.8676 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0841 1.0841 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0696 1.0696 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9995 0.9995 0.0 8 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 4.0000 0.9946 0.9946 0.0 29 -4.0000 -4.0000 0.0000 -4.0000 -4.0000 4.0000 0.9835 0.9835 0.0 42 -4.0000 -4.0000 0.0000 0.0000 4.0000 -4.0000 0.9686 0.9686 0.0 54 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 -4.0000 0.9411 0.9411 0.0 179 -4.0000 4.0000 -4.0000 0.0000 4.0000 4.0000 0.9409 0.9409 0.0 270 0.0000 -4.0000 0.0000 -4.0000 -4.0000 -4.0000 0.9353 0.9353 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.9054 0.9054 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.8113 0.8113 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.7916 0.7916 0.0 Brute Force -------------------------- Min cost was 0.791604 Number of iterations 729 Search time 1.804692 sec Parameters at best (transmm, rotdeg) 0.000 -4.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -4 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.791604 6 0.382 -4.000 0.000 0.000 0.000 0.000 0.7815387050 8 0.328 -4.000 0.000 0.000 0.000 0.000 0.7814186227 9 0.346 -4.000 0.000 0.000 0.000 0.000 0.7813724903 11 0.343 -4.000 0.000 0.000 0.000 0.000 0.7813696020 13 0.341 -4.000 0.000 0.000 0.000 0.000 0.7813689106 16 0.341 -3.000 0.000 0.000 0.000 0.000 0.7675670195 17 0.341 -1.382 0.000 0.000 0.000 0.000 0.7666522026 18 0.341 -2.135 0.000 0.000 0.000 0.000 0.7528346766 21 0.341 -1.847 0.000 0.000 0.000 0.000 0.7489196614 24 0.341 -1.803 0.000 0.000 0.000 0.000 0.7485505803 26 0.341 -1.808 0.000 0.000 0.000 0.000 0.7485374618 28 0.341 -1.810 0.000 0.000 0.000 0.000 0.7485340251 29 0.341 -1.814 0.000 0.000 0.000 0.000 0.7485289293 32 0.341 -1.815 0.000 0.000 0.000 0.000 0.7485285317 40 0.341 -1.815 -0.126 0.000 0.000 0.000 0.7485196730 41 0.341 -1.815 -0.064 0.000 0.000 0.000 0.7482795556 42 0.341 -1.815 -0.063 0.000 0.000 0.000 0.7482791747 52 0.341 -1.815 -0.063 -0.059 0.000 0.000 0.7480856345 54 0.341 -1.815 -0.063 -0.052 0.000 0.000 0.7480648462 55 0.341 -1.815 -0.063 -0.032 0.000 0.000 0.7480638515 56 0.341 -1.815 -0.063 -0.041 0.000 0.000 0.7480543199 60 0.341 -1.815 -0.063 -0.041 1.000 0.000 0.7423012952 64 0.341 -1.815 -0.063 -0.041 0.618 0.000 0.7310619607 65 0.341 -1.815 -0.063 -0.041 0.532 0.000 0.7286370907 67 0.341 -1.815 -0.063 -0.041 0.435 0.000 0.7277473015 69 0.341 -1.815 -0.063 -0.041 0.402 0.000 0.7275858630 71 0.341 -1.815 -0.063 -0.041 0.396 0.000 0.7275670500 72 0.341 -1.815 -0.063 -0.041 0.392 0.000 0.7275659033 81 0.341 -1.815 -0.063 -0.041 0.392 0.021 0.7275494663 84 0.341 -1.815 -0.063 -0.041 0.392 0.022 0.7275493081 powell nthiter 1: fret = 0.727549 91 -0.277 -1.815 -0.063 -0.041 0.392 0.022 0.7121411284 95 -0.268 -1.815 -0.063 -0.041 0.392 0.022 0.7119712825 96 -0.240 -1.815 -0.063 -0.041 0.392 0.022 0.7116761860 98 -0.238 -1.815 -0.063 -0.041 0.392 0.022 0.7116738889 107 -0.238 -1.852 -0.063 -0.041 0.392 0.022 0.7115839203 109 -0.238 -1.841 -0.063 -0.041 0.392 0.022 0.7115732987 112 -0.238 -1.839 -0.063 -0.041 0.392 0.022 0.7115732820 115 -0.238 -1.840 -0.063 -0.041 0.392 0.022 0.7115731116 122 -0.238 -1.840 -0.246 -0.041 0.392 0.022 0.7115522580 125 -0.238 -1.840 -0.310 -0.041 0.392 0.022 0.7111293795 128 -0.238 -1.840 -0.305 -0.041 0.392 0.022 0.7111109751 129 -0.238 -1.840 -0.301 -0.041 0.392 0.022 0.7111087040 139 -0.238 -1.840 -0.301 -0.068 0.392 0.022 0.7108507407 140 -0.238 -1.840 -0.301 -0.083 0.392 0.022 0.7108230108 141 -0.238 -1.840 -0.301 -0.080 0.392 0.022 0.7108224837 149 -0.238 -1.840 -0.301 -0.080 0.774 0.022 0.7100698773 150 -0.238 -1.840 -0.301 -0.080 0.602 0.022 0.7082906025 151 -0.238 -1.840 -0.301 -0.080 0.600 0.022 0.7082862977 153 -0.238 -1.840 -0.301 -0.080 0.592 0.022 0.7082792559 154 -0.238 -1.840 -0.301 -0.080 0.593 0.022 0.7082785927 163 -0.238 -1.840 -0.301 -0.080 0.593 0.072 0.7076538343 165 -0.238 -1.840 -0.301 -0.080 0.593 0.103 0.7074112120 167 -0.238 -1.840 -0.301 -0.080 0.593 0.110 0.7073891204 169 -0.238 -1.840 -0.301 -0.080 0.593 0.114 0.7073835982 powell nthiter 2: fret = 0.707384 180 -0.242 -1.840 -0.301 -0.080 0.593 0.114 0.7073816820 181 -0.243 -1.840 -0.301 -0.080 0.593 0.114 0.7073815090 189 -0.243 -1.759 -0.301 -0.080 0.593 0.114 0.7069727621 191 -0.243 -1.782 -0.301 -0.080 0.593 0.114 0.7068504374 193 -0.243 -1.784 -0.301 -0.080 0.593 0.114 0.7068471837 194 -0.243 -1.787 -0.301 -0.080 0.593 0.114 0.7068449887 196 -0.243 -1.786 -0.301 -0.080 0.593 0.114 0.7068445488 205 -0.243 -1.786 -0.269 -0.080 0.593 0.114 0.7066008527 207 -0.243 -1.786 -0.270 -0.080 0.593 0.114 0.7065996987 210 -0.243 -1.786 -0.272 -0.080 0.593 0.114 0.7065984942 211 -0.243 -1.786 -0.273 -0.080 0.593 0.114 0.7065984806 219 -0.243 -1.786 -0.273 -0.091 0.593 0.114 0.7064623887 220 -0.243 -1.786 -0.273 -0.113 0.593 0.114 0.7062979285 222 -0.243 -1.786 -0.273 -0.114 0.593 0.114 0.7062978033 231 -0.243 -1.786 -0.273 -0.114 0.652 0.114 0.7061009748 232 -0.243 -1.786 -0.273 -0.114 0.634 0.114 0.7060050546 233 -0.243 -1.786 -0.273 -0.114 0.631 0.114 0.7060047566 234 -0.243 -1.786 -0.273 -0.114 0.632 0.114 0.7060045893 235 -0.243 -1.786 -0.273 -0.114 0.633 0.114 0.7060043907 246 -0.243 -1.786 -0.273 -0.114 0.633 0.110 0.7060027343 247 -0.243 -1.786 -0.273 -0.114 0.633 0.111 0.7060024962 powell nthiter 3: fret = 0.706002 258 -0.244 -1.786 -0.273 -0.114 0.633 0.111 0.7060006537 259 -0.245 -1.786 -0.273 -0.114 0.633 0.111 0.7060001499 271 -0.245 -1.787 -0.273 -0.114 0.633 0.111 0.7059984575 281 -0.245 -1.787 -0.266 -0.114 0.633 0.111 0.7059944784 282 -0.245 -1.787 -0.268 -0.114 0.633 0.111 0.7059944087 292 -0.245 -1.787 -0.268 -0.111 0.633 0.111 0.7059782347 293 -0.245 -1.787 -0.268 -0.106 0.633 0.111 0.7059747067 294 -0.245 -1.787 -0.268 -0.108 0.633 0.111 0.7059730251 295 -0.245 -1.787 -0.268 -0.109 0.633 0.111 0.7059726194 306 -0.245 -1.787 -0.268 -0.109 0.636 0.111 0.7059691995 307 -0.245 -1.787 -0.268 -0.109 0.637 0.111 0.7059688654 320 -0.245 -1.787 -0.268 -0.109 0.637 0.113 0.7059683416 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.009437 1 -25.0 -25.0 25.0 1.038722 2 -25.0 25.0 -25.0 1.045936 3 -25.0 25.0 25.0 1.001769 4 25.0 -25.0 -25.0 1.034660 5 25.0 -25.0 25.0 0.987767 6 25.0 25.0 -25.0 1.004123 7 25.0 25.0 25.0 1.021601 REL: 8 0.705968 8.144014 1.018002 rel = 0.693484 Number of iterations 3 Min cost was 0.705968 Number of FunctionCalls 323 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.827850 sec Parameters at optimum (transmm) -0.24479 -1.78734 -0.26790 Parameters at optimum (rotdeg) -0.10857 0.63734 0.11320 Final costs ---------------- Number of surface hits 2538 WM Intensity 1688.0542 +/- 560.9297 Ctx Intensity 1770.9271 +/- 565.9273 Pct Contrast 4.9870 +/- 22.4214 Cost 0.7060 RelCost 0.8676 Reg at min cost was 0.99982 0.00921 0.01680 -0.87324; -0.01194 -0.38604 0.92241 -13.27656; -0.01498 0.92244 0.38586 11.98473; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/004/tmp.bbregister.90505/bbr.pass1.dat, type = 14 Original Reg 0.99990 -0.00181 0.01433 -0.78740; -0.01391 -0.38780 0.92164 -11.51114; -0.00389 0.92174 0.38779 12.22284; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00008 -0.01102 -0.00247 0.08584; -0.00197 -0.00176 -0.00077 1.76542; 0.01110 -0.00070 0.00193 0.23811; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 1.941596 Computing change in rh position Surface-RMS-Diff-mm 1.925116 0.142075 2.306865 mri_segreg done mri_segreg --mov bold/004/tmp.bbregister.90505/template.nii --init-reg bold/004/tmp.bbregister.90505/bbr.pass1.dat --out-reg bold/004/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/004/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/004/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/004/tmp.bbregister.90505/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 mri_segreg --mov bold/004/tmp.bbregister.90505/template.nii --init-reg bold/004/tmp.bbregister.90505/bbr.pass1.dat --out-reg bold/004/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/004/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/004/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/004/tmp.bbregister.90505/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/004/tmp.bbregister.90505/template.nii regfile bold/004/tmp.bbregister.90505/bbr.pass1.dat subject 20240801_dw204 dof 6 outregfile bold/004/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1751101392 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99982 0.00921 0.01680 -0.87324; -0.01194 -0.38604 0.92241 -13.27656; -0.01498 0.92244 0.38586 11.98473; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.997080 1 -25.0 -25.0 25.0 0.998194 2 -25.0 25.0 -25.0 0.994058 3 -25.0 25.0 25.0 0.985360 4 25.0 -25.0 -25.0 1.031044 5 25.0 -25.0 25.0 1.004973 6 25.0 25.0 -25.0 0.998100 7 25.0 25.0 25.0 1.000366 REL: 8 0.724759 8.009177 1.001147 rel = 0.723928 Initial costs ---------------- Number of surface hits 253432 WM Intensity 1678.6242 +/- 550.0974 Ctx Intensity 1764.7145 +/- 565.7770 Pct Contrast 5.0620 +/- 22.0017 Cost 0.7248 RelCost 0.7239 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.7140 0.7140 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.7129 0.7129 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.7121 0.7121 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.7117 0.7117 0.0 29 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.1000 0.7117 0.7117 0.0 31 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.7115 0.7115 0.0 37 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0000 0.7109 0.7109 0.0 40 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.7107 0.7107 0.0 112 -0.1000 0.0000 0.0000 -0.1000 0.0000 0.0000 0.7107 0.7107 0.0 118 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0000 0.7099 0.7099 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.7088 0.7088 0.0 148 -0.1000 0.0000 0.1000 0.0000 0.0000 0.0000 0.7085 0.7085 0.0 151 -0.1000 0.0000 0.1000 0.0000 0.1000 0.0000 0.7083 0.7083 0.0 325 0.0000 0.0000 -0.1000 -0.1000 -0.1000 0.0000 0.7077 0.7077 0.0 326 0.0000 0.0000 -0.1000 -0.1000 -0.1000 0.1000 0.7077 0.7077 0.0 361 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0000 0.7074 0.7074 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.7060 0.7060 0.0 Brute Force -------------------------- Min cost was 0.705968 Number of iterations 729 Search time 0.843759 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.724759 7 0.022 0.000 0.000 0.000 0.000 0.000 0.7247252135 8 0.023 0.000 0.000 0.000 0.000 0.000 0.7247246130 9 0.026 0.000 0.000 0.000 0.000 0.000 0.7247240650 11 0.028 0.000 0.000 0.000 0.000 0.000 0.7247239870 12 0.029 0.000 0.000 0.000 0.000 0.000 0.7247239145 17 0.030 0.000 0.000 0.000 0.000 0.000 0.7247239087 24 0.030 -0.202 0.000 0.000 0.000 0.000 0.7233732093 25 0.030 -0.201 0.000 0.000 0.000 0.000 0.7233731725 33 0.030 -0.201 0.058 0.000 0.000 0.000 0.7233608040 34 0.030 -0.201 0.033 0.000 0.000 0.000 0.7233367790 35 0.030 -0.201 0.032 0.000 0.000 0.000 0.7233366921 43 0.030 -0.201 0.032 -0.126 0.000 0.000 0.7233082998 44 0.030 -0.201 0.032 -0.071 0.000 0.000 0.7232332808 45 0.030 -0.201 0.032 -0.068 0.000 0.000 0.7232308401 47 0.030 -0.201 0.032 -0.057 0.000 0.000 0.7232284916 48 0.030 -0.201 0.032 -0.058 0.000 0.000 0.7232284878 49 0.030 -0.201 0.032 -0.059 0.000 0.000 0.7232283326 58 0.030 -0.201 0.032 -0.059 -0.184 0.000 0.7219119859 59 0.030 -0.201 0.032 -0.059 -0.189 0.000 0.7219074513 60 0.030 -0.201 0.032 -0.059 -0.201 0.000 0.7219005188 62 0.030 -0.201 0.032 -0.059 -0.207 0.000 0.7218996538 71 0.030 -0.201 0.032 -0.059 -0.207 -0.132 0.7214115784 73 0.030 -0.201 0.032 -0.059 -0.207 -0.119 0.7214045696 powell nthiter 1: fret = 0.721405 83 0.072 -0.201 0.032 -0.059 -0.207 -0.119 0.7213099975 85 0.075 -0.201 0.032 -0.059 -0.207 -0.119 0.7213091494 87 0.081 -0.201 0.032 -0.059 -0.207 -0.119 0.7213086412 96 0.080 -0.324 0.032 -0.059 -0.207 -0.119 0.7210380873 97 0.080 -0.303 0.032 -0.059 -0.207 -0.119 0.7210029603 98 0.080 -0.291 0.032 -0.059 -0.207 -0.119 0.7209930374 99 0.080 -0.284 0.032 -0.059 -0.207 -0.119 0.7209904368 101 0.080 -0.282 0.032 -0.059 -0.207 -0.119 0.7209903999 102 0.080 -0.281 0.032 -0.059 -0.207 -0.119 0.7209903925 110 0.080 -0.281 0.084 -0.059 -0.207 -0.119 0.7209693970 111 0.080 -0.281 0.065 -0.059 -0.207 -0.119 0.7209621838 112 0.080 -0.281 0.067 -0.059 -0.207 -0.119 0.7209620537 120 0.080 -0.281 0.067 -0.361 -0.207 -0.119 0.7197203226 123 0.080 -0.281 0.067 -0.406 -0.207 -0.119 0.7196722930 124 0.080 -0.281 0.067 -0.418 -0.207 -0.119 0.7196703922 134 0.080 -0.281 0.067 -0.418 -0.294 -0.119 0.7191619342 135 0.080 -0.281 0.067 -0.418 -0.341 -0.119 0.7191450583 136 0.080 -0.281 0.067 -0.418 -0.322 -0.119 0.7191305506 137 0.080 -0.281 0.067 -0.418 -0.323 -0.119 0.7191303991 147 0.080 -0.281 0.067 -0.418 -0.324 -0.124 0.7191299105 148 0.080 -0.281 0.067 -0.418 -0.324 -0.123 0.7191297826 150 0.130 -0.362 0.102 -0.778 -0.441 -0.128 0.7186928034 156 0.111 -0.331 0.088 -0.640 -0.396 -0.126 0.7185546012 157 0.113 -0.335 0.090 -0.656 -0.401 -0.126 0.7185415712 159 0.114 -0.336 0.090 -0.662 -0.403 -0.126 0.7185409017 160 0.113 -0.336 0.090 -0.661 -0.403 -0.126 0.7185407034 powell nthiter 2: fret = 0.718541 169 0.177 -0.336 0.090 -0.661 -0.403 -0.126 0.7181653478 170 0.186 -0.336 0.090 -0.661 -0.403 -0.126 0.7181543331 171 0.191 -0.336 0.090 -0.661 -0.403 -0.126 0.7181525769 180 0.191 -0.520 0.090 -0.661 -0.403 -0.126 0.7173055501 181 0.191 -0.508 0.090 -0.661 -0.403 -0.126 0.7172824227 182 0.191 -0.489 0.090 -0.661 -0.403 -0.126 0.7172691362 184 0.191 -0.491 0.090 -0.661 -0.403 -0.126 0.7172690460 192 0.191 -0.491 0.472 -0.661 -0.403 -0.126 0.7159567761 193 0.191 -0.491 0.339 -0.661 -0.403 -0.126 0.7152387563 195 0.191 -0.491 0.336 -0.661 -0.403 -0.126 0.7152386843 204 0.191 -0.491 0.335 -0.661 -0.403 -0.128 0.7152368625 205 0.191 -0.491 0.335 -0.661 -0.403 -0.149 0.7152307643 207 0.191 -0.491 0.335 -0.661 -0.403 -0.143 0.7152297667 208 0.191 -0.491 0.335 -0.661 -0.403 -0.144 0.7152297389 217 0.191 -0.491 0.335 -0.661 -0.436 -0.144 0.7152047580 218 0.191 -0.491 0.335 -0.661 -0.429 -0.144 0.7152021984 220 0.191 -0.491 0.335 -0.661 -0.430 -0.144 0.7152021813 222 0.191 -0.491 0.335 -0.661 -0.431 -0.144 0.7152021356 224 0.241 -0.571 0.370 -1.021 -0.547 -0.149 0.7148570809 228 0.222 -0.540 0.356 -0.884 -0.503 -0.147 0.7145508365 230 0.219 -0.535 0.354 -0.857 -0.494 -0.146 0.7145329631 231 0.218 -0.534 0.353 -0.854 -0.493 -0.146 0.7145327231 236 0.218 -0.533 0.353 -0.853 -0.493 -0.146 0.7145326920 238 0.218 -0.533 0.353 -0.852 -0.492 -0.146 0.7145326426 powell nthiter 3: fret = 0.714533 247 0.247 -0.533 0.353 -0.852 -0.492 -0.146 0.7144648913 249 0.245 -0.533 0.353 -0.852 -0.492 -0.146 0.7144642230 251 0.243 -0.533 0.353 -0.852 -0.492 -0.146 0.7144641742 259 0.243 -0.643 0.353 -0.852 -0.492 -0.146 0.7144601500 260 0.243 -0.588 0.353 -0.852 -0.492 -0.146 0.7143754527 269 0.243 -0.588 0.357 -0.852 -0.492 -0.146 0.7143635800 270 0.243 -0.588 0.394 -0.852 -0.492 -0.146 0.7142995374 273 0.243 -0.588 0.396 -0.852 -0.492 -0.146 0.7142995269 281 0.243 -0.588 0.396 -0.852 -0.492 -0.123 0.7142841863 282 0.243 -0.588 0.396 -0.852 -0.492 -0.121 0.7142837795 283 0.243 -0.588 0.396 -0.852 -0.492 -0.114 0.7142835486 285 0.243 -0.588 0.396 -0.852 -0.492 -0.117 0.7142832341 286 0.243 -0.588 0.396 -0.852 -0.492 -0.118 0.7142832237 294 0.243 -0.588 0.396 -0.852 -0.462 -0.118 0.7142773829 295 0.243 -0.588 0.396 -0.852 -0.475 -0.118 0.7142679874 296 0.243 -0.588 0.396 -0.852 -0.476 -0.118 0.7142676706 298 0.243 -0.588 0.396 -0.852 -0.477 -0.118 0.7142676434 305 0.262 -0.619 0.409 -0.989 -0.523 -0.120 0.7142038399 306 0.255 -0.608 0.404 -0.938 -0.506 -0.119 0.7141570007 307 0.255 -0.607 0.404 -0.935 -0.505 -0.119 0.7141562054 308 0.252 -0.604 0.402 -0.920 -0.501 -0.119 0.7141523483 312 0.253 -0.604 0.403 -0.923 -0.502 -0.119 0.7141521301 314 0.253 -0.604 0.403 -0.922 -0.501 -0.119 0.7141520598 powell nthiter 4: fret = 0.714152 324 0.278 -0.604 0.403 -0.922 -0.501 -0.119 0.7141261978 325 0.273 -0.604 0.403 -0.922 -0.501 -0.119 0.7141230672 326 0.271 -0.604 0.403 -0.922 -0.501 -0.119 0.7141229315 335 0.271 -0.622 0.403 -0.922 -0.501 -0.119 0.7141088610 346 0.271 -0.621 0.416 -0.922 -0.501 -0.119 0.7140889429 349 0.271 -0.621 0.428 -0.922 -0.501 -0.119 0.7140819359 350 0.271 -0.621 0.429 -0.922 -0.501 -0.119 0.7140818343 359 0.271 -0.621 0.429 -0.922 -0.501 -0.109 0.7140800167 361 0.271 -0.621 0.429 -0.922 -0.501 -0.111 0.7140798601 369 0.271 -0.621 0.429 -0.922 -0.487 -0.111 0.7140707996 370 0.271 -0.621 0.429 -0.922 -0.486 -0.111 0.7140707649 378 0.275 -0.627 0.432 -0.951 -0.495 -0.112 0.7140604549 379 0.275 -0.627 0.432 -0.948 -0.494 -0.111 0.7140597310 380 0.275 -0.626 0.431 -0.945 -0.493 -0.111 0.7140596987 383 0.275 -0.626 0.432 -0.946 -0.494 -0.111 0.7140596476 powell nthiter 5: fret = 0.714060 393 0.276 -0.626 0.432 -0.946 -0.494 -0.111 0.7140594916 403 0.276 -0.629 0.432 -0.946 -0.494 -0.111 0.7140589207 414 0.276 -0.628 0.427 -0.946 -0.494 -0.111 0.7140582534 415 0.276 -0.628 0.426 -0.946 -0.494 -0.111 0.7140581735 423 0.276 -0.628 0.426 -0.946 -0.494 -0.126 0.7140563990 424 0.276 -0.628 0.426 -0.946 -0.494 -0.121 0.7140558771 426 0.276 -0.628 0.426 -0.946 -0.494 -0.123 0.7140558742 435 0.276 -0.628 0.426 -0.946 -0.496 -0.123 0.7140552085 441 0.276 -0.628 0.426 -0.946 -0.497 -0.123 0.7140549805 451 0.277 -0.629 0.426 -0.948 -0.498 -0.123 0.7140547664 powell nthiter 6: fret = 0.714055 463 0.276 -0.629 0.426 -0.948 -0.498 -0.123 0.7140547493 473 0.276 -0.635 0.426 -0.948 -0.498 -0.123 0.7140542830 475 0.276 -0.632 0.426 -0.948 -0.498 -0.123 0.7140541171 486 0.276 -0.632 0.431 -0.948 -0.498 -0.123 0.7140541039 488 0.276 -0.632 0.428 -0.948 -0.498 -0.123 0.7140538321 508 0.276 -0.632 0.428 -0.948 -0.499 -0.123 0.7140538314 509 0.276 -0.632 0.428 -0.948 -0.500 -0.123 0.7140537197 powell nthiter 7: fret = 0.714054 551 0.276 -0.632 0.429 -0.948 -0.500 -0.123 0.7140536949 570 0.276 -0.632 0.429 -0.948 -0.499 -0.125 0.7140535729 powell nthiter 8: fret = 0.714054 606 0.276 -0.633 0.429 -0.948 -0.499 -0.125 0.7140535375 616 0.276 -0.633 0.428 -0.948 -0.499 -0.125 0.7140535153 644 0.276 -0.634 0.429 -0.950 -0.499 -0.125 0.7140533937 645 0.276 -0.634 0.429 -0.950 -0.499 -0.125 0.7140533801 powell nthiter 9: fret = 0.714053 666 0.277 -0.635 0.429 -0.950 -0.499 -0.125 0.7140533364 706 0.277 -0.635 0.429 -0.951 -0.500 -0.125 0.7140531836 powell nthiter 10: fret = 0.714053 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 0.995581 1 -25.0 -25.0 25.0 1.001693 2 -25.0 25.0 -25.0 0.993128 3 -25.0 25.0 25.0 0.981081 4 25.0 -25.0 -25.0 1.028164 5 25.0 -25.0 25.0 1.003915 6 25.0 25.0 -25.0 1.000215 7 25.0 25.0 25.0 0.998987 REL: 8 0.714053 8.002763 1.000345 rel = 0.713807 Number of iterations 10 Min cost was 0.714053 Number of FunctionCalls 771 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 37.053613 sec Parameters at optimum (transmm) 0.27691 -0.63549 0.42873 Parameters at optimum (rotdeg) -0.95095 -0.49951 -0.12494 Final costs ---------------- Number of surface hits 253432 WM Intensity 1671.1518 +/- 548.8914 Ctx Intensity 1763.1595 +/- 568.6569 Pct Contrast 5.3154 +/- 21.9216 Cost 0.7141 RelCost 0.7239 Reg at min cost was 0.99988 0.00031 0.01560 -0.73120; -0.01437 -0.37068 0.92865 -13.70915; -0.00607 0.92876 0.37063 12.62408; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/004/register.dof6.dat, type = 14 Original Reg 0.99982 0.00921 0.01680 -0.87324; -0.01194 -0.38604 0.92241 -13.27656; -0.01498 0.92244 0.38586 11.98473; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00006 0.00891 0.00121 -0.14204; 0.00243 -0.01536 -0.00624 0.43259; -0.00892 -0.00632 0.01523 -0.63935; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 1.022786 Computing change in rh position Surface-RMS-Diff-mm 1.128535 0.520462 2.367745 mri_segreg done MinCost: 0.714053 1671.151771 1763.159454 5.315391 tkregister2_cmdl --mov bold/004/template.nii.gz --reg bold/004/register.dof6.dat --noedit --ltaout bold/004/register.dof6.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/004/template.nii.gz reg file bold/004/register.dof6.dat LoadVol 0 ZeroCRAS 0 7.4.1 Diagnostic Level -1 ---- Input registration matrix -------- 0.99988 0.00031 0.01560 -0.73120; -0.01437 -0.37068 0.92865 -13.70915; -0.00607 0.92876 0.37063 12.62408; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: This is an unsigined short. INFO: loading target /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/004/template.nii.gz INFO: This is an unsigined short. Tmov: -------------------- -2.00000 0.00000 0.00000 110.00000; 0.00000 0.00000 2.00000 -64.00000; 0.00000 -2.00000 0.00000 110.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99988 0.00031 0.01560 -0.73120; -0.01437 -0.37068 0.92865 -13.70915; -0.00607 0.92876 0.37063 12.62408; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = 20240801_dw204 RegMat --------------------------- 0.99988 0.00031 0.01560 -0.73120; -0.01437 -0.37068 0.92865 -13.70915; -0.00607 0.92876 0.37063 12.62408; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue Jun 17 12:56:48 EDT 2025 Ended at Tue Jun 17 12:58:05 EDT 2025 BBR-Run-Time-Sec 77 bbregister Done To check results, run: tkregisterfv --mov bold/004/template.nii.gz --reg bold/004/register.dof6.lta --surfs --sd /Volumes/umms-hillmera/asem_ptsd/DW204 Run: 005 ---------------- Tue Jun 17 12:58:05 EDT 2025 -------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 bbregister --s 20240801_dw204 --init-coreg --6 --bold --mov bold/005/template.nii.gz --reg bold/005/register.dof6.dat --lta bold/005/register.dof6.lta --init-reg-out bold/005/init.register.dof6.dat tmp bold/005/tmp.bbregister.90625 Log file is bold/005/register.dof6.log Tue Jun 17 12:58:05 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 /Applications/freesurfer/bin/bbregister --s 20240801_dw204 --init-coreg --6 --bold --mov bold/005/template.nii.gz --reg bold/005/register.dof6.dat --lta bold/005/register.dof6.lta --init-reg-out bold/005/init.register.dof6.dat FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 FREESURFER_HOME /Applications/freesurfer mri_convert bold/005/template.nii.gz bold/005/tmp.bbregister.90625/template.nii mri_convert bold/005/template.nii.gz bold/005/tmp.bbregister.90625/template.nii reading from bold/005/template.nii.gz... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) writing to bold/005/tmp.bbregister.90625/template.nii... mri_coreg --s 20240801_dw204 --mov bold/005/tmp.bbregister.90625/template.nii --regdat bold/005/tmp.bbregister.90625/reg.init.dat --reg bold/005/tmp.bbregister.90625/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 cmdline mri_coreg --s 20240801_dw204 --mov bold/005/tmp.bbregister.90625/template.nii --regdat bold/005/tmp.bbregister.90625/reg.init.dat --reg bold/005/tmp.bbregister.90625/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov bold/005/tmp.bbregister.90625/template.nii INFO: This is an unsigined short. Reading in ref /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/brainmask.mgz Reading in and applying refmask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz Setting cras translation parameters to align volume centers Init matrix params 1.2987 -16.4649 10.9966 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 -1.29869; 0.00000 1.00000 0.00000 16.46489; 0.00000 0.00000 1.00000 -10.99657; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt 1.2987 -16.4649 10.9966 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 19550.3340 mov gstd 1.6917 1.6917 1.6917 Smoothing mov refsat = 116.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0434574524 nhits = 87627 out of 16777216, Percent Overlap: 33.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 1.29869; 0.00000 1.00000 0.00000 -16.46489; 0.00000 0.00000 1.00000 10.99657; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.50000 0.00000 0.00000 -9.24999; 0.00000 0.18649 -0.46392 89.87160; 0.00000 -0.46392 -0.18649 112.42754; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -0.70131 1.53511 4.99657 0.00000 0.00000 0.00000 -1.0475243 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: -0.701309 1.535110 4.996567 0.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0744051933 #@# 4 188 -0.70131 1.53511 4.99657 0.00000 0.00000 0.00000 -1.0744052 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.074405 #@# 4 190 0.29869 1.53511 4.99657 0.00000 0.00000 0.00000 -1.0745285 #@# 4 194 -0.08328 1.53511 4.99657 0.00000 0.00000 0.00000 -1.0746667 #@# 4 195 -0.19423 1.53511 4.99657 0.00000 0.00000 0.00000 -1.0746671 #@# 4 196 -0.14097 1.53511 4.99657 0.00000 0.00000 0.00000 -1.0746692 #@# 4 197 -0.13097 1.53511 4.99657 0.00000 0.00000 0.00000 -1.0746698 #@# 4 201 -0.13097 -0.08292 4.99657 0.00000 0.00000 0.00000 -1.0749871 #@# 4 202 -0.13097 0.48935 4.99657 0.00000 0.00000 0.00000 -1.0751505 #@# 4 206 -0.13097 0.51968 4.99657 0.00000 0.00000 0.00000 -1.0751549 #@# 4 208 -0.13097 0.57467 4.99657 0.00000 0.00000 0.00000 -1.0751562 #@# 4 209 -0.13097 0.55554 4.99657 0.00000 0.00000 0.00000 -1.0751567 #@# 4 213 -0.13097 0.55554 3.37853 0.00000 0.00000 0.00000 -1.0752759 #@# 4 214 -0.13097 0.55554 4.11913 0.00000 0.00000 0.00000 -1.0755866 #@# 4 224 -0.13097 0.55554 4.11913 -1.61803 0.00000 0.00000 -1.0762888 #@# 4 225 -0.13097 0.55554 4.11913 -1.60798 0.00000 0.00000 -1.0762941 #@# 4 229 -0.13097 0.55554 4.11913 -1.59798 0.00000 0.00000 -1.0762945 #@# 4 230 -0.13097 0.55554 4.11913 -1.54833 0.00000 0.00000 -1.0762959 #@# 4 233 -0.13097 0.55554 4.11913 -1.55833 0.00000 0.00000 -1.0762974 #@# 4 241 -0.13097 0.55554 4.11913 -1.57347 0.38197 0.00000 -1.0763093 #@# 4 243 -0.13097 0.55554 4.11913 -1.57347 0.61803 0.00000 -1.0763127 #@# 4 246 -0.13097 0.55554 4.11913 -1.57347 0.67376 0.00000 -1.0763173 #@# 4 256 -0.13097 0.55554 4.11913 -1.57347 0.67376 0.38197 -1.0763355 #@# 4 257 -0.13097 0.55554 4.11913 -1.57347 0.67376 0.26158 -1.0763381 #@# 4 258 -0.13097 0.55554 4.11913 -1.57347 0.67376 0.28209 -1.0763401 #@# 4 259 -0.13097 0.55554 4.11913 -1.57347 0.67376 0.31309 -1.0763412 powell nthiter 1: fret = -1.076341 #@# 4 270 -0.20213 0.55554 4.11913 -1.57347 0.67376 0.31309 -1.0763454 #@# 4 271 -0.19213 0.55554 4.11913 -1.57347 0.67376 0.31309 -1.0763456 #@# 4 279 -0.19213 0.28667 4.11913 -1.57347 0.67376 0.31309 -1.0763890 #@# 4 280 -0.19213 0.27667 4.11913 -1.57347 0.67376 0.31309 -1.0763891 #@# 4 286 -0.19213 0.27667 3.50109 -1.57347 0.67376 0.31309 -1.0766271 #@# 4 288 -0.19213 0.27667 3.53440 -1.57347 0.67376 0.31309 -1.0766320 #@# 4 292 -0.19213 0.27667 3.52440 -1.57347 0.67376 0.31309 -1.0766326 #@# 4 298 -0.19213 0.27667 3.52440 -2.19151 0.67376 0.31309 -1.0766659 #@# 4 300 -0.19213 0.27667 3.52440 -1.96457 0.67376 0.31309 -1.0766679 #@# 4 301 -0.19213 0.27667 3.52440 -2.05021 0.67376 0.31309 -1.0766708 #@# 4 309 -0.19213 0.27667 3.52440 -2.05021 0.05573 0.31309 -1.0766859 #@# 4 311 -0.19213 0.27667 3.52440 -2.05021 0.28391 0.31309 -1.0767056 #@# 4 321 -0.19213 0.27667 3.52440 -2.05021 0.28391 0.69505 -1.0767131 #@# 4 322 -0.19213 0.27667 3.52440 -2.05021 0.28391 0.53522 -1.0767215 powell nthiter 2: fret = -1.076722 #@# 4 333 -0.25150 0.27667 3.52440 -2.05021 0.28391 0.53522 -1.0767227 #@# 4 334 -0.23142 0.27667 3.52440 -2.05021 0.28391 0.53522 -1.0767229 #@# 4 335 -0.22142 0.27667 3.52440 -2.05021 0.28391 0.53522 -1.0767236 #@# 4 343 -0.22142 0.23541 3.52440 -2.05021 0.28391 0.53522 -1.0767261 #@# 4 353 -0.22142 0.22541 3.39496 -2.05021 0.28391 0.53522 -1.0767306 #@# 4 359 -0.22142 0.22541 3.38496 -2.05021 0.28391 0.53522 -1.0767314 #@# 4 366 -0.22142 0.22541 3.38496 -2.12111 0.28391 0.53522 -1.0767326 #@# 4 369 -0.22142 0.22541 3.38496 -2.20094 0.28391 0.53522 -1.0767349 Powell done niters total = 2 OptTimeSec 8.1 sec OptTimeMin 0.14 min nEvals 393 Final optimized parameters -0.22142126 0.22540796 3.38495922 -2.20093703 0.28390896 0.53522164 Final matrix parameters -0.2214 0.2254 3.3850 -2.2009 0.2839 0.5252 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.076734878285596 --------------------------------- Final RefRAS-to-MovRAS 0.99994 0.00934 0.00496 -0.22142; -0.00914 0.99922 -0.03840 0.22541; -0.00531 0.03836 0.99925 3.38496; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.49997 0.00248 -0.00467 -8.35227; -0.00523 0.16854 -0.47071 87.20354; 0.00076 -0.47073 -0.16855 104.82191; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters -0.2214 0.2254 3.3850 -2.2009 0.2839 0.5352 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters -0.2214 0.2254 3.3850 -2.2009 0.2839 0.5352 nhits = 86944 out of 16777216, Percent Overlap: 33.2 mri_coreg RunTimeSec 33.3 sec To check run: tkregisterfv --mov bold/005/tmp.bbregister.90625/template.nii --targ /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/brainmask.mgz --reg bold/005/tmp.bbregister.90625/mri_coreg.lta --s 20240801_dw204 --surfs mri_coreg done mri_segreg --mov bold/005/tmp.bbregister.90625/template.nii --init-reg bold/005/tmp.bbregister.90625/reg.init.dat --out-reg bold/005/tmp.bbregister.90625/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 mri_segreg --mov bold/005/tmp.bbregister.90625/template.nii --init-reg bold/005/tmp.bbregister.90625/reg.init.dat --out-reg bold/005/tmp.bbregister.90625/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/005/tmp.bbregister.90625/template.nii regfile bold/005/tmp.bbregister.90625/reg.init.dat subject 20240801_dw204 dof 6 outregfile bold/005/tmp.bbregister.90625/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750607754 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99994 0.00934 0.00496 -0.72688; -0.00152 -0.33711 0.94146 -13.81949; -0.01046 0.94142 0.33708 14.28843; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.040199 1 -25.0 -25.0 25.0 1.048243 2 -25.0 25.0 -25.0 1.034433 3 -25.0 25.0 25.0 1.000027 4 25.0 -25.0 -25.0 1.027582 5 25.0 -25.0 25.0 1.048503 6 25.0 25.0 -25.0 1.001483 7 25.0 25.0 25.0 1.052953 REL: 8 0.758853 8.253423 1.031678 rel = 0.735553 Initial costs ---------------- Number of surface hits 2538 WM Intensity 10505.6436 +/- 1391.7411 Ctx Intensity 10720.9685 +/- 1544.6429 Pct Contrast 1.7940 +/- 14.8034 Cost 0.7589 RelCost 0.7356 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0217 1.0217 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 1.0142 1.0142 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 1.0125 1.0125 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.9757 0.9757 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9686 0.9686 0.0 8 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 4.0000 0.9541 0.9541 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.9282 0.9282 0.0 16 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.0000 0.9232 0.9232 0.0 18 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 0.9017 0.9017 0.0 36 -4.0000 -4.0000 0.0000 0.0000 -4.0000 -4.0000 0.8837 0.8837 0.0 43 -4.0000 -4.0000 0.0000 0.0000 4.0000 0.0000 0.8683 0.8683 0.0 256 0.0000 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.8296 0.8296 0.0 265 0.0000 -4.0000 -4.0000 4.0000 0.0000 0.0000 0.7731 0.7731 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7584 0.7584 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.5921 0.5921 0.0 Brute Force -------------------------- Min cost was 0.592089 Number of iterations 729 Search time 0.649274 sec Parameters at best (transmm, rotdeg) 0.000 -4.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -4 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.592089 7 -0.016 -4.000 0.000 0.000 0.000 0.000 0.5920095998 9 -0.021 -4.000 0.000 0.000 0.000 0.000 0.5919999497 10 -0.026 -4.000 0.000 0.000 0.000 0.000 0.5919998217 11 -0.024 -4.000 0.000 0.000 0.000 0.000 0.5919981610 15 -0.024 -3.000 0.000 0.000 0.000 0.000 0.5430941333 20 -0.024 -2.714 0.000 0.000 0.000 0.000 0.5423845171 22 -0.024 -2.587 0.000 0.000 0.000 0.000 0.5414370108 24 -0.024 -2.564 0.000 0.000 0.000 0.000 0.5413611313 25 -0.024 -2.556 0.000 0.000 0.000 0.000 0.5413474149 27 -0.024 -2.553 0.000 0.000 0.000 0.000 0.5413447470 28 -0.024 -2.549 0.000 0.000 0.000 0.000 0.5413438297 33 -0.024 -2.549 -1.618 0.000 0.000 0.000 0.4484918089 37 -0.024 -2.549 -1.382 0.000 0.000 0.000 0.4481864141 43 -0.024 -2.549 -1.363 0.000 0.000 0.000 0.4481316037 45 -0.024 -2.549 -1.366 0.000 0.000 0.000 0.4481294989 47 -0.024 -2.549 -1.367 0.000 0.000 0.000 0.4481292965 50 -0.024 -2.549 -1.367 1.000 0.000 0.000 0.3652876859 55 -0.024 -2.549 -1.367 1.279 0.000 0.000 0.3624716630 56 -0.024 -2.549 -1.367 1.265 0.000 0.000 0.3622405738 57 -0.024 -2.549 -1.367 1.190 0.000 0.000 0.3613855181 59 -0.024 -2.549 -1.367 1.191 0.000 0.000 0.3613786211 61 -0.024 -2.549 -1.367 1.203 0.000 0.000 0.3613506756 62 -0.024 -2.549 -1.367 1.200 0.000 0.000 0.3613494954 63 -0.024 -2.549 -1.367 1.201 0.000 0.000 0.3613493523 71 -0.024 -2.549 -1.367 1.201 -0.065 0.000 0.3607110008 72 -0.024 -2.549 -1.367 1.201 -0.069 0.000 0.3606988268 73 -0.024 -2.549 -1.367 1.201 -0.084 0.000 0.3606847226 75 -0.024 -2.549 -1.367 1.201 -0.080 0.000 0.3606802788 76 -0.024 -2.549 -1.367 1.201 -0.079 0.000 0.3606794025 83 -0.024 -2.549 -1.367 1.201 -0.079 -0.618 0.3543962444 85 -0.024 -2.549 -1.367 1.201 -0.079 -0.481 0.3521973072 86 -0.024 -2.549 -1.367 1.201 -0.079 -0.402 0.3519411429 92 -0.024 -2.549 -1.367 1.201 -0.079 -0.401 0.3519410333 powell nthiter 1: fret = 0.351941 101 0.014 -2.549 -1.367 1.201 -0.079 -0.401 0.3508395418 102 0.085 -2.549 -1.367 1.201 -0.079 -0.401 0.3498008405 105 0.080 -2.549 -1.367 1.201 -0.079 -0.401 0.3497857482 106 0.075 -2.549 -1.367 1.201 -0.079 -0.401 0.3497855775 107 0.077 -2.549 -1.367 1.201 -0.079 -0.401 0.3497839399 108 0.078 -2.549 -1.367 1.201 -0.079 -0.401 0.3497837926 115 0.078 -2.520 -1.367 1.201 -0.079 -0.401 0.3491678868 117 0.078 -2.494 -1.367 1.201 -0.079 -0.401 0.3490012080 129 0.078 -2.494 -1.399 1.201 -0.079 -0.401 0.3487957813 130 0.078 -2.494 -1.413 1.201 -0.079 -0.401 0.3487831116 131 0.078 -2.494 -1.410 1.201 -0.079 -0.401 0.3487813722 140 0.078 -2.494 -1.411 1.159 -0.079 -0.401 0.3486370533 142 0.078 -2.494 -1.411 1.172 -0.079 -0.401 0.3486136413 144 0.078 -2.494 -1.411 1.169 -0.079 -0.401 0.3486123795 154 0.078 -2.494 -1.411 1.170 -0.080 -0.401 0.3486112835 155 0.078 -2.494 -1.411 1.170 -0.083 -0.401 0.3486104798 157 0.078 -2.494 -1.411 1.170 -0.082 -0.401 0.3486104222 170 0.078 -2.494 -1.411 1.170 -0.082 -0.404 0.3486092440 171 0.078 -2.494 -1.411 1.170 -0.082 -0.405 0.3486091947 powell nthiter 2: fret = 0.348609 181 0.074 -2.494 -1.411 1.170 -0.082 -0.405 0.3486049792 182 0.073 -2.494 -1.411 1.170 -0.082 -0.405 0.3486048835 183 0.072 -2.494 -1.411 1.170 -0.082 -0.405 0.3486047245 196 0.072 -2.472 -1.411 1.170 -0.082 -0.405 0.3485441581 197 0.072 -2.479 -1.411 1.170 -0.082 -0.405 0.3485237433 208 0.072 -2.479 -1.417 1.170 -0.082 -0.405 0.3485178637 229 0.072 -2.479 -1.417 1.170 -0.085 -0.405 0.3485158268 230 0.072 -2.479 -1.417 1.170 -0.086 -0.405 0.3485156232 240 0.072 -2.479 -1.417 1.170 -0.086 -0.395 0.3485130525 241 0.072 -2.479 -1.417 1.170 -0.086 -0.399 0.3485119035 243 0.072 -2.479 -1.417 1.170 -0.086 -0.400 0.3485118004 245 0.066 -2.464 -1.424 1.170 -0.089 -0.395 0.3485039985 251 0.068 -2.469 -1.422 1.170 -0.088 -0.396 0.3484968587 253 0.068 -2.470 -1.421 1.170 -0.088 -0.397 0.3484967573 254 0.068 -2.470 -1.421 1.170 -0.088 -0.397 0.3484964440 255 0.069 -2.471 -1.421 1.170 -0.088 -0.397 0.3484958120 257 0.069 -2.471 -1.421 1.170 -0.088 -0.397 0.3484956996 258 0.069 -2.471 -1.421 1.170 -0.088 -0.397 0.3484956824 259 0.069 -2.471 -1.421 1.170 -0.088 -0.397 0.3484956538 powell nthiter 3: fret = 0.348496 270 0.068 -2.471 -1.421 1.170 -0.088 -0.397 0.3484943743 271 0.065 -2.471 -1.421 1.170 -0.088 -0.397 0.3484937506 273 0.066 -2.471 -1.421 1.170 -0.088 -0.397 0.3484936854 283 0.066 -2.471 -1.421 1.170 -0.088 -0.393 0.3484914792 293 0.066 -2.471 -1.434 1.170 -0.088 -0.393 0.3484907214 294 0.066 -2.471 -1.428 1.170 -0.088 -0.393 0.3484869568 296 0.066 -2.471 -1.427 1.170 -0.088 -0.393 0.3484869463 307 0.066 -2.471 -1.426 1.171 -0.088 -0.393 0.3484856822 308 0.066 -2.471 -1.426 1.172 -0.088 -0.393 0.3484831027 310 0.066 -2.471 -1.426 1.175 -0.088 -0.393 0.3484813080 321 0.066 -2.471 -1.426 1.175 -0.083 -0.393 0.3484788812 322 0.066 -2.471 -1.426 1.175 -0.084 -0.393 0.3484788508 329 0.064 -2.465 -1.428 1.175 -0.086 -0.391 0.3484759132 331 0.063 -2.463 -1.429 1.175 -0.086 -0.390 0.3484758583 332 0.064 -2.464 -1.429 1.175 -0.086 -0.391 0.3484758085 334 0.064 -2.464 -1.429 1.175 -0.086 -0.391 0.3484757557 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.025558 1 -25.0 -25.0 25.0 1.002847 2 -25.0 25.0 -25.0 1.028295 3 -25.0 25.0 25.0 1.012094 4 25.0 -25.0 -25.0 1.016839 5 25.0 -25.0 25.0 1.017684 6 25.0 25.0 -25.0 1.035982 7 25.0 25.0 25.0 1.035965 REL: 8 0.348476 8.175264 1.021908 rel = 0.341005 Number of iterations 3 Min cost was 0.348476 Number of FunctionCalls 339 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.307772 sec Parameters at optimum (transmm) 0.06356 -2.46396 -1.42879 Parameters at optimum (rotdeg) 1.17474 -0.08581 -0.39077 Final costs ---------------- Number of surface hits 2537 WM Intensity 10052.3581 +/- 1496.8635 Ctx Intensity 10849.9670 +/- 1785.4605 Pct Contrast 7.0727 +/- 17.8396 Cost 0.3485 RelCost 0.7356 Reg at min cost was 0.99993 0.00551 0.01079 -0.78051; -0.00812 -0.35638 0.93430 -16.56805; -0.00900 0.93432 0.35631 12.57221; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/005/tmp.bbregister.90625/bbr.pass1.dat, type = 14 Original Reg 0.99994 0.00934 0.00496 -0.72688; -0.00152 -0.33711 0.94146 -13.81949; -0.01046 0.94142 0.33708 14.28843; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00002 0.00383 -0.00584 0.05362; 0.00660 0.01928 0.00716 2.74856; -0.00147 0.00710 -0.01924 1.71622; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.681846 Computing change in rh position Surface-RMS-Diff-mm 2.839010 0.766947 4.675581 mri_segreg done mri_segreg --mov bold/005/tmp.bbregister.90625/template.nii --init-reg bold/005/tmp.bbregister.90625/bbr.pass1.dat --out-reg bold/005/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/005/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/005/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/005/tmp.bbregister.90625/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 mri_segreg --mov bold/005/tmp.bbregister.90625/template.nii --init-reg bold/005/tmp.bbregister.90625/bbr.pass1.dat --out-reg bold/005/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/005/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/005/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/005/tmp.bbregister.90625/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/005/tmp.bbregister.90625/template.nii regfile bold/005/tmp.bbregister.90625/bbr.pass1.dat subject 20240801_dw204 dof 6 outregfile bold/005/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750736279 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99993 0.00551 0.01079 -0.78051; -0.00812 -0.35638 0.93430 -16.56805; -0.00900 0.93432 0.35631 12.57221; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.030812 1 -25.0 -25.0 25.0 1.015702 2 -25.0 25.0 -25.0 1.016602 3 -25.0 25.0 25.0 1.018973 4 25.0 -25.0 -25.0 1.005331 5 25.0 -25.0 25.0 1.039818 6 25.0 25.0 -25.0 1.016044 7 25.0 25.0 25.0 1.016702 REL: 8 0.367043 8.159984 1.019998 rel = 0.359847 Initial costs ---------------- Number of surface hits 253296 WM Intensity 10058.4096 +/- 1495.8438 Ctx Intensity 10858.9933 +/- 1714.6212 Pct Contrast 7.2217 +/- 16.7806 Cost 0.3670 RelCost 0.3598 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.3538 0.3538 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.3522 0.3522 0.0 18 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 -0.1000 0.3519 0.3519 0.0 36 -0.1000 -0.1000 0.0000 0.0000 -0.1000 -0.1000 0.3512 0.3512 0.0 91 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.3510 0.3510 0.0 117 -0.1000 0.0000 0.0000 0.0000 -0.1000 -0.1000 0.3508 0.3508 0.0 118 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0000 0.3505 0.3505 0.0 283 0.0000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.3502 0.3502 0.0 334 0.0000 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.3500 0.3500 0.0 335 0.0000 0.0000 -0.1000 0.0000 -0.1000 0.1000 0.3499 0.3499 0.0 337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.3496 0.3496 0.0 338 0.0000 0.0000 -0.1000 0.0000 0.0000 0.1000 0.3494 0.3494 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3485 0.3485 0.0 Brute Force -------------------------- Min cost was 0.348476 Number of iterations 729 Search time 0.652016 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.367043 7 0.102 0.000 0.000 0.000 0.000 0.000 0.3664065974 8 0.103 0.000 0.000 0.000 0.000 0.000 0.3664065110 16 0.103 0.059 0.000 0.000 0.000 0.000 0.3661994225 18 0.103 0.061 0.000 0.000 0.000 0.000 0.3661994009 26 0.103 0.061 -0.093 0.000 0.000 0.000 0.3658985260 27 0.103 0.061 -0.071 0.000 0.000 0.000 0.3658817443 28 0.103 0.061 -0.075 0.000 0.000 0.000 0.3658809217 37 0.103 0.061 -0.076 0.109 0.000 0.000 0.3654225822 39 0.103 0.061 -0.076 0.117 0.000 0.000 0.3654203197 48 0.103 0.061 -0.076 0.117 0.004 0.000 0.3654116104 49 0.103 0.061 -0.076 0.117 0.021 0.000 0.3653951060 50 0.103 0.061 -0.076 0.117 0.022 0.000 0.3653949541 51 0.103 0.061 -0.076 0.117 0.023 0.000 0.3653948757 53 0.103 0.061 -0.076 0.117 0.024 0.000 0.3653948637 61 0.103 0.061 -0.076 0.117 0.024 0.130 0.3647344784 62 0.103 0.061 -0.076 0.117 0.024 0.134 0.3647334094 63 0.103 0.061 -0.076 0.117 0.024 0.135 0.3647332590 powell nthiter 1: fret = 0.364733 74 0.119 0.061 -0.076 0.117 0.024 0.135 0.3646976392 75 0.128 0.061 -0.076 0.117 0.024 0.135 0.3646917254 76 0.129 0.061 -0.076 0.117 0.024 0.135 0.3646916933 85 0.130 0.071 -0.076 0.117 0.024 0.135 0.3646915511 86 0.130 0.066 -0.076 0.117 0.024 0.135 0.3646897076 95 0.130 0.066 -0.122 0.117 0.024 0.135 0.3646269979 96 0.130 0.066 -0.110 0.117 0.024 0.135 0.3646198556 97 0.130 0.066 -0.111 0.117 0.024 0.135 0.3646198044 105 0.130 0.066 -0.111 0.113 0.024 0.135 0.3646196869 106 0.130 0.066 -0.111 0.114 0.024 0.135 0.3646196756 114 0.130 0.066 -0.111 0.114 0.009 0.135 0.3646147225 115 0.130 0.066 -0.111 0.114 0.014 0.135 0.3646140327 116 0.130 0.066 -0.111 0.114 0.013 0.135 0.3646139677 124 0.130 0.066 -0.111 0.114 0.013 0.137 0.3646124387 125 0.130 0.066 -0.111 0.114 0.013 0.148 0.3646065602 130 0.130 0.066 -0.111 0.114 0.013 0.150 0.3646064670 powell nthiter 2: fret = 0.364606 158 0.130 0.066 -0.112 0.114 0.013 0.150 0.3646063691 166 0.130 0.066 -0.112 0.112 0.013 0.150 0.3646061747 powell nthiter 3: fret = 0.364606 196 0.129 0.066 -0.112 0.112 0.013 0.150 0.3646061521 powell nthiter 4: fret = 0.364606 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.030709 1 -25.0 -25.0 25.0 1.015448 2 -25.0 25.0 -25.0 1.015648 3 -25.0 25.0 25.0 1.019551 4 25.0 -25.0 -25.0 1.005418 5 25.0 -25.0 25.0 1.040386 6 25.0 25.0 -25.0 1.018061 7 25.0 25.0 25.0 1.016080 REL: 8 0.364606 8.161300 1.020163 rel = 0.3574 Number of iterations 4 Min cost was 0.364606 Number of FunctionCalls 298 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 14.137565 sec Parameters at optimum (transmm) 0.12893 0.06579 -0.11139 Parameters at optimum (rotdeg) 0.11172 0.01250 0.15024 Final costs ---------------- Number of surface hits 253298 WM Intensity 10053.5140 +/- 1494.8854 Ctx Intensity 10861.0680 +/- 1717.4192 Pct Contrast 7.2874 +/- 16.7782 Cost 0.3646 RelCost 0.3598 Reg at min cost was 0.99994 0.00665 0.00842 -0.60532; -0.00548 -0.35819 0.93363 -16.52873; -0.00923 0.93363 0.35813 12.42866; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/005/register.dof6.dat, type = 14 Original Reg 0.99993 0.00551 0.01079 -0.78051; -0.00812 -0.35638 0.93430 -16.56805; -0.00900 0.93432 0.35631 12.57221; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00002 -0.00114 0.00237 -0.17518; -0.00264 0.00180 0.00067 -0.03932; 0.00023 0.00070 -0.00182 0.14355; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.192010 Computing change in rh position Surface-RMS-Diff-mm 0.219083 0.078474 0.392167 mri_segreg done MinCost: 0.364606 10053.514017 10861.068040 7.287380 tkregister2_cmdl --mov bold/005/template.nii.gz --reg bold/005/register.dof6.dat --noedit --ltaout bold/005/register.dof6.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/005/template.nii.gz reg file bold/005/register.dof6.dat LoadVol 0 ZeroCRAS 0 7.4.1 Diagnostic Level -1 ---- Input registration matrix -------- 0.99994 0.00665 0.00842 -0.60532; -0.00548 -0.35819 0.93363 -16.52873; -0.00923 0.93363 0.35813 12.42866; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: This is an unsigined short. INFO: loading target /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/005/template.nii.gz INFO: This is an unsigined short. Tmov: -------------------- -2.00000 0.00000 0.00000 110.00000; 0.00000 0.00000 2.00000 -60.00000; 0.00000 -2.00000 0.00000 110.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99994 0.00665 0.00842 -0.60532; -0.00548 -0.35819 0.93363 -16.52873; -0.00923 0.93363 0.35813 12.42866; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = 20240801_dw204 RegMat --------------------------- 0.99994 0.00665 0.00842 -0.60532; -0.00548 -0.35819 0.93363 -16.52873; -0.00923 0.93363 0.35813 12.42866; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue Jun 17 12:58:05 EDT 2025 Ended at Tue Jun 17 12:59:00 EDT 2025 BBR-Run-Time-Sec 55 bbregister Done To check results, run: tkregisterfv --mov bold/005/template.nii.gz --reg bold/005/register.dof6.lta --surfs --sd /Volumes/umms-hillmera/asem_ptsd/DW204 Run: 006 ---------------- Tue Jun 17 12:59:00 EDT 2025 -------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 bbregister --s 20240801_dw204 --init-coreg --6 --bold --mov bold/006/template.nii.gz --reg bold/006/register.dof6.dat --lta bold/006/register.dof6.lta --init-reg-out bold/006/init.register.dof6.dat tmp bold/006/tmp.bbregister.90729 Log file is bold/006/register.dof6.log Tue Jun 17 12:59:01 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 /Applications/freesurfer/bin/bbregister --s 20240801_dw204 --init-coreg --6 --bold --mov bold/006/template.nii.gz --reg bold/006/register.dof6.dat --lta bold/006/register.dof6.lta --init-reg-out bold/006/init.register.dof6.dat FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 FREESURFER_HOME /Applications/freesurfer mri_convert bold/006/template.nii.gz bold/006/tmp.bbregister.90729/template.nii mri_convert bold/006/template.nii.gz bold/006/tmp.bbregister.90729/template.nii reading from bold/006/template.nii.gz... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) writing to bold/006/tmp.bbregister.90729/template.nii... mri_coreg --s 20240801_dw204 --mov bold/006/tmp.bbregister.90729/template.nii --regdat bold/006/tmp.bbregister.90729/reg.init.dat --reg bold/006/tmp.bbregister.90729/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 cmdline mri_coreg --s 20240801_dw204 --mov bold/006/tmp.bbregister.90729/template.nii --regdat bold/006/tmp.bbregister.90729/reg.init.dat --reg bold/006/tmp.bbregister.90729/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov bold/006/tmp.bbregister.90729/template.nii INFO: This is an unsigined short. Reading in ref /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/brainmask.mgz Reading in and applying refmask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz Setting cras translation parameters to align volume centers Init matrix params 1.2987 -16.4649 10.9966 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 -1.29869; 0.00000 1.00000 0.00000 16.46489; 0.00000 0.00000 1.00000 -10.99657; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt 1.2987 -16.4649 10.9966 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 19080.3340 mov gstd 1.6917 1.6917 1.6917 Smoothing mov refsat = 116.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0435881911 nhits = 87627 out of 16777216, Percent Overlap: 33.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 1.29869; 0.00000 1.00000 0.00000 -16.46489; 0.00000 0.00000 1.00000 10.99657; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.50000 0.00000 0.00000 -9.24999; 0.00000 0.18649 -0.46392 89.87160; 0.00000 -0.46392 -0.18649 112.42754; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -0.70131 1.53511 4.99657 0.00000 0.00000 0.00000 -1.0470696 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: -0.701309 1.535110 4.996567 0.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0738484859 #@# 4 188 -0.70131 1.53511 4.99657 0.00000 0.00000 0.00000 -1.0738485 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.073848 #@# 4 190 0.29869 1.53511 4.99657 0.00000 0.00000 0.00000 -1.0740778 #@# 4 194 -0.08328 1.53511 4.99657 0.00000 0.00000 0.00000 -1.0741391 #@# 4 195 -0.02362 1.53511 4.99657 0.00000 0.00000 0.00000 -1.0741401 #@# 4 199 -0.00497 1.53511 4.99657 0.00000 0.00000 0.00000 -1.0741405 #@# 4 203 -0.00497 -0.08292 4.99657 0.00000 0.00000 0.00000 -1.0750916 #@# 4 207 -0.00497 0.15314 4.99657 0.00000 0.00000 0.00000 -1.0750947 #@# 4 208 -0.00497 0.05003 4.99657 0.00000 0.00000 0.00000 -1.0750952 #@# 4 210 -0.00497 0.04003 4.99657 0.00000 0.00000 0.00000 -1.0750957 #@# 4 211 -0.00497 -0.00693 4.99657 0.00000 0.00000 0.00000 -1.0750967 #@# 4 213 -0.00497 0.01155 4.99657 0.00000 0.00000 0.00000 -1.0750973 #@# 4 217 -0.00497 0.01155 3.37853 0.00000 0.00000 0.00000 -1.0757053 #@# 4 218 -0.00497 0.01155 3.84138 0.00000 0.00000 0.00000 -1.0758821 #@# 4 223 -0.00497 0.01155 3.86051 0.00000 0.00000 0.00000 -1.0758822 #@# 4 224 -0.00497 0.01155 3.87051 0.00000 0.00000 0.00000 -1.0758832 #@# 4 225 -0.00497 0.01155 3.88602 0.00000 0.00000 0.00000 -1.0758837 #@# 4 231 -0.00497 0.01155 3.88602 -0.61803 0.00000 0.00000 -1.0759367 #@# 4 233 -0.00497 0.01155 3.88602 -0.51932 0.00000 0.00000 -1.0759484 #@# 4 238 -0.00497 0.01155 3.88602 -0.53372 0.00000 0.00000 -1.0759494 #@# 4 239 -0.00497 0.01155 3.88602 -0.54372 0.00000 0.00000 -1.0759501 #@# 4 241 -0.00497 0.01155 3.88602 -0.54372 1.00000 0.00000 -1.0760199 #@# 4 246 -0.00497 0.01155 3.88602 -0.54372 0.85572 0.00000 -1.0760237 #@# 4 247 -0.00497 0.01155 3.88602 -0.54372 0.86572 0.00000 -1.0760279 #@# 4 248 -0.00497 0.01155 3.88602 -0.54372 0.92386 0.00000 -1.0760287 #@# 4 252 -0.00497 0.01155 3.88602 -0.54372 0.91322 0.00000 -1.0760297 #@# 4 258 -0.00497 0.01155 3.88602 -0.54372 0.91322 0.38197 -1.0760776 #@# 4 259 -0.00497 0.01155 3.88602 -0.54372 0.91322 0.39197 -1.0760784 #@# 4 261 -0.00497 0.01155 3.88602 -0.54372 0.91322 0.47312 -1.0760850 #@# 4 262 -0.00497 0.01155 3.88602 -0.54372 0.91322 0.53083 -1.0760869 #@# 4 264 -0.00497 0.01155 3.88602 -0.54372 0.91322 0.51858 -1.0760872 powell nthiter 1: fret = -1.076087 #@# 4 273 -0.13965 0.01155 3.88602 -0.54372 0.91322 0.51858 -1.0761000 #@# 4 274 -0.12562 0.01155 3.88602 -0.54372 0.91322 0.51858 -1.0761020 #@# 4 295 -0.12562 -0.00980 3.63478 -0.54372 0.91322 0.51858 -1.0761310 #@# 4 296 -0.12562 -0.00980 3.65373 -0.54372 0.91322 0.51858 -1.0761323 #@# 4 297 -0.12562 -0.00980 3.68781 -0.54372 0.91322 0.51858 -1.0761368 #@# 4 299 -0.12562 -0.00980 3.71673 -0.54372 0.91322 0.51858 -1.0761385 #@# 4 301 -0.12562 -0.00980 3.70673 -0.54372 0.91322 0.51858 -1.0761387 #@# 4 308 -0.12562 -0.00980 3.70673 -0.64410 0.91322 0.51858 -1.0761422 #@# 4 333 -0.12562 -0.00980 3.70673 -0.64410 0.91322 0.45393 -1.0761428 #@# 4 338 -0.12562 -0.00980 3.70673 -0.64410 0.91322 0.44215 -1.0761446 Powell done niters total = 1 OptTimeSec 6.1 sec OptTimeMin 0.10 min nEvals 338 Final optimized parameters -0.12561677 -0.00979713 3.70673060 -0.64410079 0.91321844 0.44214717 Final matrix parameters -0.1256 -0.0098 3.7067 -0.6441 0.9132 0.4421 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.076144564822549 --------------------------------- Final RefRAS-to-MovRAS 0.99984 0.00772 0.01594 -0.12562; -0.00754 0.99991 -0.01124 -0.00980; -0.01602 0.01112 0.99981 3.70673; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.49992 0.00797 -0.00386 -9.18486; -0.00648 0.18124 -0.46595 85.30074; 0.00603 -0.46593 -0.18132 104.96597; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters -0.1256 -0.0098 3.7067 -0.6441 0.9132 0.4421 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters -0.1256 -0.0098 3.7067 -0.6441 0.9132 0.4421 nhits = 86872 out of 16777216, Percent Overlap: 33.1 mri_coreg RunTimeSec 31.4 sec To check run: tkregisterfv --mov bold/006/tmp.bbregister.90729/template.nii --targ /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/brainmask.mgz --reg bold/006/tmp.bbregister.90729/mri_coreg.lta --s 20240801_dw204 --surfs mri_coreg done mri_segreg --mov bold/006/tmp.bbregister.90729/template.nii --init-reg bold/006/tmp.bbregister.90729/reg.init.dat --out-reg bold/006/tmp.bbregister.90729/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 mri_segreg --mov bold/006/tmp.bbregister.90729/template.nii --init-reg bold/006/tmp.bbregister.90729/reg.init.dat --out-reg bold/006/tmp.bbregister.90729/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/006/tmp.bbregister.90729/template.nii regfile bold/006/tmp.bbregister.90729/reg.init.dat subject 20240801_dw204 dof 6 outregfile bold/006/tmp.bbregister.90729/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750994104 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99984 0.00772 0.01594 -0.66266; -0.01206 -0.36264 0.93185 -14.21968; -0.01297 0.93190 0.36249 13.94318; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.047670 1 -25.0 -25.0 25.0 1.056163 2 -25.0 25.0 -25.0 1.023267 3 -25.0 25.0 25.0 1.018317 4 25.0 -25.0 -25.0 1.055329 5 25.0 -25.0 25.0 1.053969 6 25.0 25.0 -25.0 0.984058 7 25.0 25.0 25.0 1.035900 REL: 8 0.739563 8.274674 1.034334 rel = 0.715014 Initial costs ---------------- Number of surface hits 2537 WM Intensity 10498.8536 +/- 1402.3584 Ctx Intensity 10721.6968 +/- 1566.0013 Pct Contrast 1.8012 +/- 14.7202 Cost 0.7396 RelCost 0.7150 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0177 1.0177 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.9710 0.9710 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9548 0.9548 0.0 8 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 4.0000 0.9525 0.9525 0.0 14 -4.0000 -4.0000 -4.0000 0.0000 0.0000 4.0000 0.9481 0.9481 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.9405 0.9405 0.0 18 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 0.9250 0.9250 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.9178 0.9178 0.0 36 -4.0000 -4.0000 0.0000 0.0000 -4.0000 -4.0000 0.8875 0.8875 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8828 0.8828 0.0 43 -4.0000 -4.0000 0.0000 0.0000 4.0000 0.0000 0.8662 0.8662 0.0 256 0.0000 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.8305 0.8305 0.0 265 0.0000 -4.0000 -4.0000 4.0000 0.0000 0.0000 0.7679 0.7679 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6140 0.6140 0.0 Brute Force -------------------------- Min cost was 0.614034 Number of iterations 729 Search time 0.845793 sec Parameters at best (transmm, rotdeg) 0.000 -4.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -4 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.614034 6 0.382 -4.000 0.000 0.000 0.000 0.000 0.6137855925 8 0.618 -4.000 0.000 0.000 0.000 0.000 0.6125490817 13 0.624 -4.000 0.000 0.000 0.000 0.000 0.6125377053 15 0.630 -4.000 0.000 0.000 0.000 0.000 0.6125316239 17 0.631 -4.000 0.000 0.000 0.000 0.000 0.6125311478 20 0.631 -3.000 0.000 0.000 0.000 0.000 0.5393225514 23 0.631 -2.382 0.000 0.000 0.000 0.000 0.5385953389 25 0.631 -2.659 0.000 0.000 0.000 0.000 0.5342873498 28 0.631 -2.664 0.000 0.000 0.000 0.000 0.5342778885 35 0.631 -2.665 -1.618 0.000 0.000 0.000 0.4690075478 40 0.631 -2.665 -1.000 0.000 0.000 0.000 0.4654796727 44 0.631 -2.665 -1.093 0.000 0.000 0.000 0.4648090381 47 0.631 -2.665 -1.100 0.000 0.000 0.000 0.4648037389 52 0.631 -2.665 -1.100 1.000 0.000 0.000 0.4011195619 57 0.631 -2.665 -1.100 1.137 0.000 0.000 0.3996480449 58 0.631 -2.665 -1.100 1.169 0.000 0.000 0.3993708194 60 0.631 -2.665 -1.100 1.232 0.000 0.000 0.3989760802 62 0.631 -2.665 -1.100 1.239 0.000 0.000 0.3989531930 64 0.631 -2.665 -1.100 1.238 0.000 0.000 0.3989516174 74 0.631 -2.665 -1.100 1.238 -0.050 0.000 0.3986456701 76 0.631 -2.665 -1.100 1.238 -0.044 0.000 0.3986374430 80 0.631 -2.665 -1.100 1.238 -0.046 0.000 0.3986371805 88 0.631 -2.665 -1.100 1.238 -0.046 0.149 0.3978382912 90 0.631 -2.665 -1.100 1.238 -0.046 0.148 0.3978379938 powell nthiter 1: fret = 0.397838 97 0.013 -2.665 -1.100 1.238 -0.046 0.148 0.3699400277 101 0.103 -2.665 -1.100 1.238 -0.046 0.148 0.3696817308 103 0.068 -2.665 -1.100 1.238 -0.046 0.148 0.3695888330 105 0.074 -2.665 -1.100 1.238 -0.046 0.148 0.3695815125 106 0.078 -2.665 -1.100 1.238 -0.046 0.148 0.3695800843 107 0.077 -2.665 -1.100 1.238 -0.046 0.148 0.3695797526 115 0.077 -2.526 -1.100 1.238 -0.046 0.148 0.3679722926 116 0.077 -2.525 -1.100 1.238 -0.046 0.148 0.3679663053 119 0.077 -2.522 -1.100 1.238 -0.046 0.148 0.3679527551 128 0.077 -2.522 -1.718 1.238 -0.046 0.148 0.3677517272 130 0.077 -2.522 -1.412 1.238 -0.046 0.148 0.3600761498 132 0.077 -2.522 -1.435 1.238 -0.046 0.148 0.3600014723 134 0.077 -2.522 -1.456 1.238 -0.046 0.148 0.3599482803 137 0.077 -2.522 -1.457 1.238 -0.046 0.148 0.3599479313 145 0.077 -2.522 -1.457 1.276 -0.046 0.148 0.3597314373 146 0.077 -2.522 -1.457 1.304 -0.046 0.148 0.3596547822 148 0.077 -2.522 -1.457 1.307 -0.046 0.148 0.3596535084 149 0.077 -2.522 -1.457 1.308 -0.046 0.148 0.3596534432 150 0.077 -2.522 -1.457 1.309 -0.046 0.148 0.3596532958 159 0.077 -2.522 -1.457 1.309 -0.087 0.148 0.3592627214 161 0.077 -2.522 -1.457 1.309 -0.126 0.148 0.3589779610 163 0.077 -2.522 -1.457 1.309 -0.140 0.148 0.3589534729 164 0.077 -2.522 -1.457 1.309 -0.141 0.148 0.3589530966 172 0.077 -2.522 -1.457 1.309 -0.141 0.036 0.3584057501 173 0.077 -2.522 -1.457 1.309 -0.141 0.038 0.3583872754 174 0.077 -2.522 -1.457 1.309 -0.141 0.071 0.3582587937 176 0.077 -2.522 -1.457 1.309 -0.141 0.070 0.3582587215 powell nthiter 2: fret = 0.358259 185 -0.097 -2.522 -1.457 1.309 -0.141 0.070 0.3565564740 186 -0.094 -2.522 -1.457 1.309 -0.141 0.070 0.3565320534 187 -0.050 -2.522 -1.457 1.309 -0.141 0.070 0.3563907664 189 -0.063 -2.522 -1.457 1.309 -0.141 0.070 0.3563510817 191 -0.061 -2.522 -1.457 1.309 -0.141 0.070 0.3563490826 193 -0.059 -2.522 -1.457 1.309 -0.141 0.070 0.3563474262 194 -0.058 -2.522 -1.457 1.309 -0.141 0.070 0.3563471356 211 -0.058 -2.522 -1.465 1.309 -0.141 0.070 0.3562601653 213 -0.058 -2.522 -1.513 1.309 -0.141 0.070 0.3560658701 214 -0.058 -2.522 -1.504 1.309 -0.141 0.070 0.3560341878 215 -0.058 -2.522 -1.500 1.309 -0.141 0.070 0.3560325319 216 -0.058 -2.522 -1.501 1.309 -0.141 0.070 0.3560322640 225 -0.058 -2.522 -1.501 1.338 -0.141 0.070 0.3559924528 226 -0.058 -2.522 -1.501 1.332 -0.141 0.070 0.3559893157 227 -0.058 -2.522 -1.501 1.331 -0.141 0.070 0.3559892968 237 -0.058 -2.522 -1.501 1.331 -0.142 0.070 0.3559881530 247 -0.058 -2.522 -1.501 1.331 -0.142 0.068 0.3559800987 248 -0.058 -2.522 -1.501 1.331 -0.142 0.053 0.3559618625 250 -0.058 -2.522 -1.501 1.331 -0.142 0.056 0.3559603165 powell nthiter 3: fret = 0.355960 262 -0.051 -2.522 -1.501 1.331 -0.142 0.056 0.3559372799 265 -0.050 -2.522 -1.501 1.331 -0.142 0.056 0.3559370195 274 -0.050 -2.512 -1.501 1.331 -0.142 0.056 0.3559228271 277 -0.050 -2.511 -1.501 1.331 -0.142 0.056 0.3559228184 287 -0.050 -2.511 -1.517 1.331 -0.142 0.056 0.3558852468 297 -0.050 -2.511 -1.517 1.346 -0.142 0.056 0.3558625734 299 -0.050 -2.511 -1.517 1.350 -0.142 0.056 0.3558618468 301 -0.050 -2.511 -1.517 1.351 -0.142 0.056 0.3558616626 311 -0.050 -2.511 -1.517 1.351 -0.141 0.056 0.3558616320 322 -0.050 -2.511 -1.517 1.351 -0.141 0.054 0.3558615038 powell nthiter 4: fret = 0.355862 333 -0.049 -2.511 -1.517 1.351 -0.141 0.054 0.3558599123 344 -0.049 -2.510 -1.517 1.351 -0.141 0.054 0.3558589652 345 -0.049 -2.508 -1.517 1.351 -0.141 0.054 0.3558581583 356 -0.049 -2.508 -1.525 1.351 -0.141 0.054 0.3558500265 368 -0.049 -2.508 -1.525 1.352 -0.141 0.054 0.3558492695 379 -0.049 -2.508 -1.525 1.352 -0.143 0.054 0.3558490579 390 -0.049 -2.508 -1.525 1.352 -0.143 0.053 0.3558486944 391 -0.049 -2.508 -1.525 1.352 -0.143 0.052 0.3558485326 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.037502 1 -25.0 -25.0 25.0 0.994916 2 -25.0 25.0 -25.0 1.036604 3 -25.0 25.0 25.0 0.983415 4 25.0 -25.0 -25.0 1.008049 5 25.0 -25.0 25.0 1.012762 6 25.0 25.0 -25.0 1.030635 7 25.0 25.0 25.0 1.037362 REL: 8 0.355849 8.141246 1.017656 rel = 0.349675 Number of iterations 4 Min cost was 0.355849 Number of FunctionCalls 393 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.459492 sec Parameters at optimum (transmm) -0.04918 -2.50817 -1.52528 Parameters at optimum (rotdeg) 1.35233 -0.14279 0.05217 Final costs ---------------- Number of surface hits 2536 WM Intensity 10073.8229 +/- 1563.5612 Ctx Intensity 10848.5101 +/- 1851.7592 Pct Contrast 6.8275 +/- 17.9226 Cost 0.3558 RelCost 0.7150 Reg at min cost was 0.99988 0.00577 0.01414 -0.73249; -0.01084 -0.38453 0.92305 -17.05358; -0.01076 0.92310 0.38442 12.07673; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/006/tmp.bbregister.90729/bbr.pass1.dat, type = 14 Original Reg 0.99984 0.00772 0.01594 -0.66266; -0.01206 -0.36264 0.93185 -14.21968; -0.01297 0.93190 0.36249 13.94318; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00004 0.00195 0.00180 0.06984; -0.00122 0.02189 0.00880 2.83390; -0.00221 0.00880 -0.02193 1.86645; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.949744 Computing change in rh position Surface-RMS-Diff-mm 2.928499 0.877845 5.035408 mri_segreg done mri_segreg --mov bold/006/tmp.bbregister.90729/template.nii --init-reg bold/006/tmp.bbregister.90729/bbr.pass1.dat --out-reg bold/006/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/006/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/006/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/006/tmp.bbregister.90729/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 mri_segreg --mov bold/006/tmp.bbregister.90729/template.nii --init-reg bold/006/tmp.bbregister.90729/bbr.pass1.dat --out-reg bold/006/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/006/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/006/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/006/tmp.bbregister.90729/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/006/tmp.bbregister.90729/template.nii regfile bold/006/tmp.bbregister.90729/bbr.pass1.dat subject 20240801_dw204 dof 6 outregfile bold/006/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750482207 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99988 0.00577 0.01414 -0.73249; -0.01084 -0.38453 0.92305 -17.05358; -0.01076 0.92310 0.38442 12.07673; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.028903 1 -25.0 -25.0 25.0 1.015080 2 -25.0 25.0 -25.0 1.017464 3 -25.0 25.0 25.0 1.010050 4 25.0 -25.0 -25.0 1.003312 5 25.0 -25.0 25.0 1.036908 6 25.0 25.0 -25.0 1.018581 7 25.0 25.0 25.0 1.012340 REL: 8 0.369953 8.142638 1.017830 rel = 0.363473 Initial costs ---------------- Number of surface hits 253225 WM Intensity 10072.0352 +/- 1553.2525 Ctx Intensity 10854.8436 +/- 1766.5411 Pct Contrast 7.0435 +/- 16.8308 Cost 0.3700 RelCost 0.3635 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.3627 0.3627 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.3618 0.3618 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.3610 0.3610 0.0 11 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.3607 0.3607 0.0 14 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.3607 0.3607 0.0 27 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 -0.1000 0.3604 0.3604 0.0 28 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.0000 0.3595 0.3595 0.0 29 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.1000 0.3590 0.3590 0.0 31 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.3586 0.3586 0.0 56 -0.1000 -0.1000 0.1000 -0.1000 -0.1000 0.1000 0.3581 0.3581 0.0 57 -0.1000 -0.1000 0.1000 -0.1000 0.0000 -0.1000 0.3573 0.3573 0.0 60 -0.1000 -0.1000 0.1000 -0.1000 0.1000 -0.1000 0.3573 0.3573 0.0 138 -0.1000 0.0000 0.1000 -0.1000 0.0000 -0.1000 0.3564 0.3564 0.0 141 -0.1000 0.0000 0.1000 -0.1000 0.1000 -0.1000 0.3561 0.3561 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3558 0.3558 0.0 Brute Force -------------------------- Min cost was 0.355849 Number of iterations 729 Search time 1.824398 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.369953 7 0.109 0.000 0.000 0.000 0.000 0.000 0.3691885299 8 0.108 0.000 0.000 0.000 0.000 0.000 0.3691883042 9 0.107 0.000 0.000 0.000 0.000 0.000 0.3691881000 12 0.106 0.000 0.000 0.000 0.000 0.000 0.3691880755 20 0.106 0.165 0.000 0.000 0.000 0.000 0.3672793427 22 0.106 0.161 0.000 0.000 0.000 0.000 0.3672720666 27 0.106 0.162 0.000 0.000 0.000 0.000 0.3672719655 35 0.106 0.162 0.018 0.000 0.000 0.000 0.3672300710 36 0.106 0.162 0.027 0.000 0.000 0.000 0.3672264633 37 0.106 0.162 0.025 0.000 0.000 0.000 0.3672262423 45 0.106 0.162 0.025 -0.086 0.000 0.000 0.3669275635 46 0.106 0.162 0.025 -0.080 0.000 0.000 0.3669242263 47 0.106 0.162 0.025 -0.077 0.000 0.000 0.3669240273 48 0.106 0.162 0.025 -0.078 0.000 0.000 0.3669239361 55 0.106 0.162 0.025 -0.078 0.026 0.000 0.3668801707 57 0.106 0.162 0.025 -0.078 0.025 0.000 0.3668800067 65 0.106 0.162 0.025 -0.078 0.025 0.113 0.3664850447 67 0.106 0.162 0.025 -0.078 0.025 0.118 0.3664842396 68 0.106 0.162 0.025 -0.078 0.025 0.119 0.3664841959 powell nthiter 1: fret = 0.366484 77 0.142 0.162 0.025 -0.078 0.025 0.119 0.3663893370 78 0.145 0.162 0.025 -0.078 0.025 0.119 0.3663887196 88 0.145 0.164 0.025 -0.078 0.025 0.119 0.3663849501 89 0.145 0.165 0.025 -0.078 0.025 0.119 0.3663839593 97 0.145 0.165 0.033 -0.078 0.025 0.119 0.3663677843 98 0.145 0.165 0.045 -0.078 0.025 0.119 0.3663621961 99 0.145 0.165 0.042 -0.078 0.025 0.119 0.3663617999 109 0.145 0.165 0.043 -0.087 0.025 0.119 0.3663601119 112 0.145 0.165 0.043 -0.090 0.025 0.119 0.3663599076 122 0.145 0.165 0.043 -0.091 0.027 0.119 0.3663595143 123 0.145 0.165 0.043 -0.091 0.028 0.119 0.3663594730 133 0.145 0.165 0.043 -0.091 0.029 0.124 0.3663579395 134 0.145 0.165 0.043 -0.091 0.029 0.126 0.3663578546 135 0.145 0.165 0.043 -0.091 0.029 0.127 0.3663577750 141 0.145 0.165 0.043 -0.091 0.029 0.128 0.3663575659 powell nthiter 2: fret = 0.366358 151 0.146 0.165 0.043 -0.091 0.029 0.128 0.3663574826 159 0.146 0.166 0.043 -0.091 0.029 0.128 0.3663567726 169 0.146 0.166 0.045 -0.091 0.029 0.128 0.3663561823 170 0.146 0.166 0.046 -0.091 0.029 0.128 0.3663561161 181 0.146 0.166 0.046 -0.092 0.029 0.128 0.3663560629 192 0.146 0.166 0.046 -0.092 0.027 0.128 0.3663557686 powell nthiter 3: fret = 0.366356 240 0.146 0.166 0.046 -0.093 0.027 0.128 0.3663557340 powell nthiter 4: fret = 0.366356 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.030501 1 -25.0 -25.0 25.0 1.016082 2 -25.0 25.0 -25.0 1.017560 3 -25.0 25.0 25.0 1.010056 4 25.0 -25.0 -25.0 1.004102 5 25.0 -25.0 25.0 1.038258 6 25.0 25.0 -25.0 1.019246 7 25.0 25.0 25.0 1.013897 REL: 8 0.366356 8.149701 1.018713 rel = 0.359626 Number of iterations 4 Min cost was 0.366356 Number of FunctionCalls 321 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 16.239585 sec Parameters at optimum (transmm) 0.14636 0.16641 0.04715 Parameters at optimum (rotdeg) -0.09270 0.02703 0.12764 Final costs ---------------- Number of surface hits 253247 WM Intensity 10077.1455 +/- 1540.0117 Ctx Intensity 10869.9902 +/- 1739.6788 Pct Contrast 7.1744 +/- 16.4864 Cost 0.3664 RelCost 0.3635 Reg at min cost was 0.99990 0.00705 0.01226 -0.54247; -0.00863 -0.38302 0.92370 -16.86919; -0.01121 0.92371 0.38292 12.15180; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/006/register.dof6.dat, type = 14 Original Reg 0.99988 0.00577 0.01414 -0.73249; -0.01084 -0.38453 0.92305 -17.05358; -0.01076 0.92310 0.38442 12.07673; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00002 -0.00129 0.00188 -0.19002; -0.00221 -0.00151 -0.00065 -0.18439; 0.00045 -0.00062 0.00150 -0.07507; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.195844 Computing change in rh position Surface-RMS-Diff-mm 0.234660 0.086461 0.433504 mri_segreg done MinCost: 0.366356 10077.145498 10869.990209 7.174436 tkregister2_cmdl --mov bold/006/template.nii.gz --reg bold/006/register.dof6.dat --noedit --ltaout bold/006/register.dof6.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/006/template.nii.gz reg file bold/006/register.dof6.dat LoadVol 0 ZeroCRAS 0 7.4.1 Diagnostic Level -1 ---- Input registration matrix -------- 0.99990 0.00705 0.01226 -0.54247; -0.00863 -0.38302 0.92370 -16.86919; -0.01121 0.92371 0.38292 12.15180; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: This is an unsigined short. INFO: loading target /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/006/template.nii.gz INFO: This is an unsigined short. Tmov: -------------------- -2.00000 0.00000 0.00000 110.00000; 0.00000 0.00000 2.00000 -60.00000; 0.00000 -2.00000 0.00000 110.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99990 0.00705 0.01226 -0.54247; -0.00863 -0.38302 0.92370 -16.86919; -0.01121 0.92371 0.38292 12.15180; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = 20240801_dw204 RegMat --------------------------- 0.99990 0.00705 0.01226 -0.54247; -0.00863 -0.38302 0.92370 -16.86919; -0.01121 0.92371 0.38292 12.15180; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue Jun 17 12:59:01 EDT 2025 Ended at Tue Jun 17 12:59:57 EDT 2025 BBR-Run-Time-Sec 56 bbregister Done To check results, run: tkregisterfv --mov bold/006/template.nii.gz --reg bold/006/register.dof6.lta --surfs --sd /Volumes/umms-hillmera/asem_ptsd/DW204 Run: 007 ---------------- Tue Jun 17 12:59:57 EDT 2025 -------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 bbregister --s 20240801_dw204 --init-coreg --6 --bold --mov bold/007/template.nii.gz --reg bold/007/register.dof6.dat --lta bold/007/register.dof6.lta --init-reg-out bold/007/init.register.dof6.dat tmp bold/007/tmp.bbregister.90831 Log file is bold/007/register.dof6.log Tue Jun 17 12:59:58 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 /Applications/freesurfer/bin/bbregister --s 20240801_dw204 --init-coreg --6 --bold --mov bold/007/template.nii.gz --reg bold/007/register.dof6.dat --lta bold/007/register.dof6.lta --init-reg-out bold/007/init.register.dof6.dat FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 FREESURFER_HOME /Applications/freesurfer mri_convert bold/007/template.nii.gz bold/007/tmp.bbregister.90831/template.nii mri_convert bold/007/template.nii.gz bold/007/tmp.bbregister.90831/template.nii reading from bold/007/template.nii.gz... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) writing to bold/007/tmp.bbregister.90831/template.nii... mri_coreg --s 20240801_dw204 --mov bold/007/tmp.bbregister.90831/template.nii --regdat bold/007/tmp.bbregister.90831/reg.init.dat --reg bold/007/tmp.bbregister.90831/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 cmdline mri_coreg --s 20240801_dw204 --mov bold/007/tmp.bbregister.90831/template.nii --regdat bold/007/tmp.bbregister.90831/reg.init.dat --reg bold/007/tmp.bbregister.90831/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov bold/007/tmp.bbregister.90831/template.nii INFO: This is an unsigined short. Reading in ref /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/brainmask.mgz Reading in and applying refmask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz Setting cras translation parameters to align volume centers Init matrix params 1.2987 -16.4649 10.9966 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 -1.29869; 0.00000 1.00000 0.00000 16.46489; 0.00000 0.00000 1.00000 -10.99657; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt 1.2987 -16.4649 10.9966 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 19167.3340 mov gstd 1.6917 1.6917 1.6917 Smoothing mov refsat = 116.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0438693757 nhits = 87627 out of 16777216, Percent Overlap: 33.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 1.29869; 0.00000 1.00000 0.00000 -16.46489; 0.00000 0.00000 1.00000 10.99657; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.50000 0.00000 0.00000 -9.24999; 0.00000 0.18649 -0.46392 89.87160; 0.00000 -0.46392 -0.18649 112.42754; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -0.70131 1.53511 4.99657 0.00000 0.00000 0.00000 -1.0473183 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: -0.701309 1.535110 4.996567 0.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0738788843 #@# 4 188 -0.70131 1.53511 4.99657 0.00000 0.00000 0.00000 -1.0738789 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.073879 #@# 4 194 -0.31934 1.53511 4.99657 0.00000 0.00000 0.00000 -1.0740396 #@# 4 196 -0.25123 1.53511 4.99657 0.00000 0.00000 0.00000 -1.0740448 #@# 4 203 -0.26123 -0.08292 4.99657 0.00000 0.00000 0.00000 -1.0751046 #@# 4 216 -0.26123 -0.07292 4.37853 0.00000 0.00000 0.00000 -1.0754126 #@# 4 218 -0.26123 -0.07292 4.28243 0.00000 0.00000 0.00000 -1.0754188 #@# 4 219 -0.26123 -0.07292 4.27243 0.00000 0.00000 0.00000 -1.0754195 #@# 4 225 -0.26123 -0.07292 4.27243 -1.61803 0.00000 0.00000 -1.0759900 #@# 4 226 -0.26123 -0.07292 4.27243 -1.45252 0.00000 0.00000 -1.0760089 #@# 4 230 -0.26123 -0.07292 4.27243 -1.34965 0.00000 0.00000 -1.0760127 #@# 4 250 -0.26123 -0.07292 4.27243 -1.34965 0.00000 0.38197 -1.0760242 #@# 4 251 -0.26123 -0.07292 4.27243 -1.34965 0.00000 0.23381 -1.0760359 #@# 4 253 -0.26123 -0.07292 4.27243 -1.34965 0.00000 0.26148 -1.0760380 powell nthiter 1: fret = -1.076038 #@# 4 264 -0.28473 -0.07292 4.27243 -1.34965 0.00000 0.26148 -1.0760391 #@# 4 284 -0.28473 -0.07292 3.65439 -1.34965 0.00000 0.26148 -1.0761956 #@# 4 286 -0.28473 -0.07292 3.76038 -1.34965 0.00000 0.26148 -1.0761986 #@# 4 292 -0.28473 -0.07292 3.77038 -1.34965 0.00000 0.26148 -1.0761998 #@# 4 297 -0.28473 -0.07292 3.77038 -1.96768 0.00000 0.26148 -1.0762367 #@# 4 299 -0.28473 -0.07292 3.77038 -1.75923 0.00000 0.26148 -1.0762559 #@# 4 301 -0.28473 -0.07292 3.77038 -1.79140 0.00000 0.26148 -1.0762590 #@# 4 311 -0.28473 -0.07292 3.77038 -1.79140 -0.08523 0.26148 -1.0762613 #@# 4 312 -0.28473 -0.07292 3.77038 -1.79140 -0.12452 0.26148 -1.0762653 #@# 4 326 -0.28473 -0.07292 3.77038 -1.79140 -0.13452 0.28148 -1.0762675 powell nthiter 2: fret = -1.076267 #@# 4 349 -0.28473 -0.09139 3.77038 -1.79140 -0.13452 0.28148 -1.0762684 #@# 4 350 -0.28473 -0.10281 3.77038 -1.79140 -0.13452 0.28148 -1.0762696 #@# 4 357 -0.28473 -0.10281 3.62907 -1.79140 -0.13452 0.28148 -1.0762733 #@# 4 362 -0.28473 -0.10281 3.63907 -1.79140 -0.13452 0.28148 -1.0762750 #@# 4 363 -0.28473 -0.10281 3.65404 -1.79140 -0.13452 0.28148 -1.0762773 #@# 4 371 -0.28473 -0.10281 3.65404 -1.86222 -0.13452 0.28148 -1.0762794 #@# 4 372 -0.28473 -0.10281 3.65404 -1.87222 -0.13452 0.28148 -1.0762801 #@# 4 393 -0.28473 -0.10281 3.65404 -1.87222 -0.13452 0.30479 -1.0762821 #@# 4 395 -0.28473 -0.10281 3.65404 -1.87222 -0.13452 0.32862 -1.0762835 Powell done niters total = 2 OptTimeSec 8.3 sec OptTimeMin 0.14 min nEvals 397 Final optimized parameters -0.28472814 -0.10280543 3.65404320 -1.87222075 -0.13452418 0.32862362 Final matrix parameters -0.2847 -0.1028 3.6540 -1.8722 -0.1345 0.3186 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.076283444269887 --------------------------------- Final RefRAS-to-MovRAS 0.99998 0.00574 -0.00235 -0.28473; -0.00581 0.99945 -0.03267 -0.10281; 0.00216 0.03268 0.99946 3.65404; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.49999 -0.00117 -0.00287 -8.02533; -0.00229 0.17124 -0.46976 86.48891; -0.00209 -0.46976 -0.17123 105.50453; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters -0.2847 -0.1028 3.6540 -1.8722 -0.1345 0.3286 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters -0.2847 -0.1028 3.6540 -1.8722 -0.1345 0.3286 nhits = 87012 out of 16777216, Percent Overlap: 33.2 mri_coreg RunTimeSec 33.8 sec To check run: tkregisterfv --mov bold/007/tmp.bbregister.90831/template.nii --targ /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/brainmask.mgz --reg bold/007/tmp.bbregister.90831/mri_coreg.lta --s 20240801_dw204 --surfs mri_coreg done mri_segreg --mov bold/007/tmp.bbregister.90831/template.nii --init-reg bold/007/tmp.bbregister.90831/reg.init.dat --out-reg bold/007/tmp.bbregister.90831/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 mri_segreg --mov bold/007/tmp.bbregister.90831/template.nii --init-reg bold/007/tmp.bbregister.90831/reg.init.dat --out-reg bold/007/tmp.bbregister.90831/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/007/tmp.bbregister.90831/template.nii regfile bold/007/tmp.bbregister.90831/reg.init.dat subject 20240801_dw204 dof 6 outregfile bold/007/tmp.bbregister.90831/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750545696 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99998 0.00574 -0.00235 -0.91219; 0.00417 -0.34246 0.93952 -13.61832; -0.00458 0.93952 0.34247 14.03028; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.033981 1 -25.0 -25.0 25.0 1.051164 2 -25.0 25.0 -25.0 1.026992 3 -25.0 25.0 25.0 1.014595 4 25.0 -25.0 -25.0 1.027097 5 25.0 -25.0 25.0 1.043542 6 25.0 25.0 -25.0 1.011195 7 25.0 25.0 25.0 1.038754 REL: 8 0.745713 8.247320 1.030915 rel = 0.723351 Initial costs ---------------- Number of surface hits 2538 WM Intensity 10505.4359 +/- 1386.6702 Ctx Intensity 10752.8138 +/- 1548.3620 Pct Contrast 2.0641 +/- 14.8969 Cost 0.7457 RelCost 0.7234 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9997 0.9997 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.9914 0.9914 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9524 0.9524 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8990 0.8990 0.0 36 -4.0000 -4.0000 0.0000 0.0000 -4.0000 -4.0000 0.8792 0.8792 0.0 43 -4.0000 -4.0000 0.0000 0.0000 4.0000 0.0000 0.8594 0.8594 0.0 255 0.0000 -4.0000 -4.0000 0.0000 0.0000 -4.0000 0.8593 0.8593 0.0 256 0.0000 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.7977 0.7977 0.0 265 0.0000 -4.0000 -4.0000 4.0000 0.0000 0.0000 0.7419 0.7419 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7359 0.7359 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6227 0.6227 0.0 Brute Force -------------------------- Min cost was 0.622713 Number of iterations 729 Search time 0.647978 sec Parameters at best (transmm, rotdeg) 0.000 -4.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -4 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.622713 6 0.382 -4.000 0.000 0.000 0.000 0.000 0.6136027977 8 0.361 -4.000 0.000 0.000 0.000 0.000 0.6135222529 9 0.341 -4.000 0.000 0.000 0.000 0.000 0.6134547912 13 0.338 -4.000 0.000 0.000 0.000 0.000 0.6134535686 19 0.338 -3.000 0.000 0.000 0.000 0.000 0.5489019250 22 0.338 -2.382 0.000 0.000 0.000 0.000 0.5218559243 27 0.338 -2.385 0.000 0.000 0.000 0.000 0.5218550190 32 0.338 -2.385 -1.618 0.000 0.000 0.000 0.4249627300 36 0.338 -2.385 -1.382 0.000 0.000 0.000 0.4221741988 38 0.338 -2.385 -1.402 0.000 0.000 0.000 0.4221377919 39 0.338 -2.385 -1.412 0.000 0.000 0.000 0.4221302633 42 0.338 -2.385 -1.411 0.000 0.000 0.000 0.4221299467 45 0.338 -2.385 -1.411 1.000 0.000 0.000 0.3636579288 48 0.338 -2.385 -1.411 1.618 0.000 0.000 0.3589839629 50 0.338 -2.385 -1.411 1.359 0.000 0.000 0.3556233528 51 0.338 -2.385 -1.411 1.375 0.000 0.000 0.3554496343 52 0.338 -2.385 -1.411 1.421 0.000 0.000 0.3554399375 54 0.338 -2.385 -1.411 1.399 0.000 0.000 0.3553710491 56 0.338 -2.385 -1.411 1.396 0.000 0.000 0.3553693108 58 0.338 -2.385 -1.411 1.393 0.000 0.000 0.3553685832 60 0.338 -2.385 -1.411 1.392 0.000 0.000 0.3553685706 70 0.338 -2.385 -1.411 1.392 -0.033 0.000 0.3553539532 72 0.338 -2.385 -1.411 1.392 -0.018 0.000 0.3553150108 79 0.338 -2.385 -1.411 1.392 -0.018 -0.618 0.3505355520 81 0.338 -2.385 -1.411 1.392 -0.018 -0.469 0.3484902963 82 0.338 -2.385 -1.411 1.392 -0.018 -0.393 0.3483520933 83 0.338 -2.385 -1.411 1.392 -0.018 -0.414 0.3483297200 85 0.338 -2.385 -1.411 1.392 -0.018 -0.418 0.3483296838 88 0.338 -2.385 -1.411 1.392 -0.018 -0.417 0.3483294367 powell nthiter 1: fret = 0.348329 97 0.211 -2.385 -1.411 1.392 -0.018 -0.417 0.3476040275 98 0.231 -2.385 -1.411 1.392 -0.018 -0.417 0.3475299806 99 0.243 -2.385 -1.411 1.392 -0.018 -0.417 0.3475232029 100 0.239 -2.385 -1.411 1.392 -0.018 -0.417 0.3475226734 101 0.240 -2.385 -1.411 1.392 -0.018 -0.417 0.3475225661 109 0.240 -2.334 -1.411 1.392 -0.018 -0.417 0.3471464941 111 0.240 -2.335 -1.411 1.392 -0.018 -0.417 0.3471456275 112 0.240 -2.338 -1.411 1.392 -0.018 -0.417 0.3471446731 114 0.240 -2.337 -1.411 1.392 -0.018 -0.417 0.3471444867 120 0.240 -2.337 -2.029 1.392 -0.018 -0.417 0.3462625767 122 0.240 -2.337 -1.733 1.392 -0.018 -0.417 0.3409467980 123 0.240 -2.337 -1.732 1.392 -0.018 -0.417 0.3409445316 124 0.240 -2.337 -1.715 1.392 -0.018 -0.417 0.3409183394 126 0.240 -2.337 -1.688 1.392 -0.018 -0.417 0.3409094371 127 0.240 -2.337 -1.695 1.392 -0.018 -0.417 0.3409090045 129 0.240 -2.337 -1.703 1.392 -0.018 -0.417 0.3409084854 131 0.240 -2.337 -1.700 1.392 -0.018 -0.417 0.3409079329 132 0.240 -2.337 -1.699 1.392 -0.018 -0.417 0.3409079215 140 0.240 -2.337 -1.699 1.455 -0.018 -0.417 0.3405418823 142 0.240 -2.337 -1.699 1.447 -0.018 -0.417 0.3405215602 144 0.240 -2.337 -1.699 1.443 -0.018 -0.417 0.3405183034 145 0.240 -2.337 -1.699 1.441 -0.018 -0.417 0.3405171020 147 0.240 -2.337 -1.699 1.439 -0.018 -0.417 0.3405162955 155 0.240 -2.337 -1.699 1.439 -0.092 -0.417 0.3396179113 158 0.240 -2.337 -1.699 1.439 -0.093 -0.417 0.3396176647 168 0.240 -2.337 -1.699 1.439 -0.093 -0.411 0.3396106115 169 0.240 -2.337 -1.699 1.439 -0.093 -0.402 0.3396079405 170 0.240 -2.337 -1.699 1.439 -0.093 -0.404 0.3396075499 powell nthiter 2: fret = 0.339608 181 0.205 -2.337 -1.699 1.439 -0.093 -0.404 0.3394355389 190 0.204 -2.389 -1.699 1.439 -0.093 -0.404 0.3389524802 192 0.204 -2.406 -1.699 1.439 -0.093 -0.404 0.3389077218 202 0.204 -2.406 -1.711 1.439 -0.093 -0.404 0.3388917571 203 0.204 -2.406 -1.712 1.439 -0.093 -0.404 0.3388912603 204 0.204 -2.406 -1.715 1.439 -0.093 -0.404 0.3388909894 206 0.204 -2.406 -1.714 1.439 -0.093 -0.404 0.3388908048 214 0.204 -2.406 -1.714 1.476 -0.093 -0.404 0.3385472151 216 0.204 -2.406 -1.714 1.486 -0.093 -0.404 0.3385010376 217 0.204 -2.406 -1.714 1.491 -0.093 -0.404 0.3384916040 219 0.204 -2.406 -1.714 1.493 -0.093 -0.404 0.3384899336 220 0.204 -2.406 -1.714 1.494 -0.093 -0.404 0.3384898693 228 0.204 -2.406 -1.714 1.494 -0.118 -0.404 0.3384580159 229 0.204 -2.406 -1.714 1.494 -0.115 -0.404 0.3384477142 230 0.204 -2.406 -1.714 1.494 -0.108 -0.404 0.3384336478 243 0.204 -2.406 -1.714 1.494 -0.108 -0.415 0.3384309716 245 0.204 -2.406 -1.714 1.494 -0.108 -0.411 0.3384297494 248 0.204 -2.406 -1.714 1.494 -0.108 -0.410 0.3384297325 powell nthiter 3: fret = 0.338430 258 0.196 -2.406 -1.714 1.494 -0.108 -0.410 0.3384232975 261 0.197 -2.406 -1.714 1.494 -0.108 -0.410 0.3384230112 268 0.197 -2.407 -1.714 1.494 -0.108 -0.410 0.3384170195 271 0.197 -2.414 -1.714 1.494 -0.108 -0.410 0.3383987235 273 0.197 -2.412 -1.714 1.494 -0.108 -0.410 0.3383964731 275 0.197 -2.411 -1.714 1.494 -0.108 -0.410 0.3383957933 283 0.197 -2.411 -1.724 1.494 -0.108 -0.410 0.3383742416 284 0.197 -2.411 -1.728 1.494 -0.108 -0.410 0.3383714283 317 0.197 -2.411 -1.728 1.494 -0.108 -0.406 0.3383692999 powell nthiter 4: fret = 0.338369 329 0.199 -2.411 -1.728 1.494 -0.108 -0.406 0.3383683370 340 0.199 -2.413 -1.728 1.494 -0.108 -0.406 0.3383648334 351 0.199 -2.413 -1.730 1.494 -0.108 -0.406 0.3383644825 362 0.199 -2.413 -1.730 1.495 -0.108 -0.406 0.3383639917 373 0.199 -2.413 -1.730 1.495 -0.110 -0.406 0.3383638840 385 0.199 -2.413 -1.730 1.495 -0.110 -0.404 0.3383612901 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.049706 1 -25.0 -25.0 25.0 1.004813 2 -25.0 25.0 -25.0 1.030740 3 -25.0 25.0 25.0 1.025374 4 25.0 -25.0 -25.0 0.986681 5 25.0 -25.0 25.0 0.991752 6 25.0 25.0 -25.0 1.019546 7 25.0 25.0 25.0 1.014508 REL: 8 0.338361 8.123119 1.015390 rel = 0.333233 Number of iterations 4 Min cost was 0.338361 Number of FunctionCalls 387 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.347459 sec Parameters at optimum (transmm) 0.19862 -2.41266 -1.73014 Parameters at optimum (rotdeg) 1.49506 -0.11036 -0.40432 Final costs ---------------- Number of surface hits 2537 WM Intensity 10051.4182 +/- 1528.7893 Ctx Intensity 10880.0312 +/- 1818.9549 Pct Contrast 7.3924 +/- 17.9881 Cost 0.3384 RelCost 0.7234 Reg at min cost was 0.99999 0.00135 0.00351 -0.83853; -0.00277 -0.36687 0.93027 -16.38543; -0.00255 0.93027 0.36687 11.93827; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/007/tmp.bbregister.90831/bbr.pass1.dat, type = 14 Original Reg 0.99998 0.00574 -0.00235 -0.91219; 0.00417 -0.34246 0.93952 -13.61832; -0.00458 0.93952 0.34247 14.03028; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00001 0.00438 -0.00586 -0.07367; 0.00694 0.02441 0.00926 2.76711; -0.00204 0.00925 -0.02439 2.09201; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.847648 Computing change in rh position Surface-RMS-Diff-mm 2.989484 0.920611 5.241168 mri_segreg done mri_segreg --mov bold/007/tmp.bbregister.90831/template.nii --init-reg bold/007/tmp.bbregister.90831/bbr.pass1.dat --out-reg bold/007/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/007/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/007/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/007/tmp.bbregister.90831/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 mri_segreg --mov bold/007/tmp.bbregister.90831/template.nii --init-reg bold/007/tmp.bbregister.90831/bbr.pass1.dat --out-reg bold/007/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/007/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/007/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/007/tmp.bbregister.90831/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/007/tmp.bbregister.90831/template.nii regfile bold/007/tmp.bbregister.90831/bbr.pass1.dat subject 20240801_dw204 dof 6 outregfile bold/007/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750704867 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99999 0.00135 0.00351 -0.83853; -0.00277 -0.36687 0.93027 -16.38543; -0.00255 0.93027 0.36687 11.93827; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.033455 1 -25.0 -25.0 25.0 1.012746 2 -25.0 25.0 -25.0 1.014096 3 -25.0 25.0 25.0 1.015240 4 25.0 -25.0 -25.0 1.003680 5 25.0 -25.0 25.0 1.028437 6 25.0 25.0 -25.0 1.009985 7 25.0 25.0 25.0 1.010905 REL: 8 0.349699 8.128544 1.016068 rel = 0.344169 Initial costs ---------------- Number of surface hits 253311 WM Intensity 10043.1400 +/- 1512.7932 Ctx Intensity 10898.3340 +/- 1746.5345 Pct Contrast 7.6976 +/- 17.0671 Cost 0.3497 RelCost 0.3442 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.3443 0.3443 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.3440 0.3440 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.3428 0.3428 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.3426 0.3426 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.3422 0.3422 0.0 10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.3420 0.3420 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.3418 0.3418 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.3412 0.3412 0.0 19 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.0000 0.3408 0.3408 0.0 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.3406 0.3406 0.0 40 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.3404 0.3404 0.0 46 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.0000 0.3402 0.3402 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3399 0.3399 0.0 291 0.0000 -0.1000 0.0000 0.1000 0.0000 -0.1000 0.3397 0.3397 0.0 292 0.0000 -0.1000 0.0000 0.1000 0.0000 0.0000 0.3394 0.3394 0.0 337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.3393 0.3393 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3384 0.3384 0.0 Brute Force -------------------------- Min cost was 0.338361 Number of iterations 729 Search time 0.651987 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.349699 7 0.059 0.000 0.000 0.000 0.000 0.000 0.3493670031 8 0.071 0.000 0.000 0.000 0.000 0.000 0.3493505487 9 0.076 0.000 0.000 0.000 0.000 0.000 0.3493498865 10 0.074 0.000 0.000 0.000 0.000 0.000 0.3493496593 18 0.074 0.113 0.000 0.000 0.000 0.000 0.3484819698 27 0.074 0.113 -0.050 0.000 0.000 0.000 0.3484234433 28 0.074 0.113 -0.033 0.000 0.000 0.000 0.3484043588 30 0.074 0.113 -0.032 0.000 0.000 0.000 0.3484042552 39 0.074 0.113 -0.032 -0.241 0.000 0.000 0.3457049976 40 0.074 0.113 -0.032 -0.240 0.000 0.000 0.3457049077 41 0.074 0.113 -0.032 -0.239 0.000 0.000 0.3457048887 50 0.074 0.113 -0.032 -0.239 0.033 0.000 0.3456800705 51 0.074 0.113 -0.032 -0.239 0.024 0.000 0.3456697474 52 0.074 0.113 -0.032 -0.239 0.022 0.000 0.3456693721 61 0.074 0.113 -0.032 -0.239 0.022 0.052 0.3456018072 63 0.074 0.113 -0.032 -0.239 0.022 0.049 0.3456016208 64 0.074 0.113 -0.032 -0.239 0.022 0.048 0.3456015802 powell nthiter 1: fret = 0.345602 74 0.071 0.113 -0.032 -0.239 0.022 0.047 0.3456004646 75 0.070 0.113 -0.032 -0.239 0.022 0.047 0.3456004513 83 0.070 0.140 -0.032 -0.239 0.022 0.047 0.3455702842 84 0.070 0.135 -0.032 -0.239 0.022 0.047 0.3455686613 86 0.070 0.136 -0.032 -0.239 0.022 0.047 0.3455686342 94 0.070 0.136 -0.000 -0.239 0.022 0.047 0.3454668160 95 0.070 0.136 0.009 -0.239 0.022 0.047 0.3454579694 96 0.070 0.136 0.013 -0.239 0.022 0.047 0.3454561782 97 0.070 0.136 0.015 -0.239 0.022 0.047 0.3454561568 105 0.070 0.136 0.015 -0.264 0.022 0.047 0.3454483548 106 0.070 0.136 0.015 -0.254 0.022 0.047 0.3454393636 108 0.070 0.136 0.015 -0.255 0.022 0.047 0.3454391779 118 0.070 0.136 0.015 -0.255 0.023 0.047 0.3454386585 119 0.070 0.136 0.015 -0.255 0.025 0.047 0.3454380865 131 0.070 0.136 0.015 -0.255 0.025 0.039 0.3454354053 powell nthiter 2: fret = 0.345435 143 0.068 0.136 0.015 -0.255 0.025 0.040 0.3454350167 152 0.067 0.135 0.015 -0.255 0.025 0.040 0.3454342338 153 0.067 0.130 0.015 -0.255 0.025 0.040 0.3454320926 165 0.067 0.130 0.016 -0.255 0.025 0.040 0.3454320744 173 0.067 0.130 0.016 -0.254 0.025 0.040 0.3454318980 183 0.067 0.130 0.016 -0.254 0.023 0.040 0.3454318495 195 0.067 0.130 0.016 -0.254 0.022 0.039 0.3454317997 powell nthiter 3: fret = 0.345432 213 0.067 0.129 0.016 -0.254 0.022 0.039 0.3454317928 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.034196 1 -25.0 -25.0 25.0 1.013053 2 -25.0 25.0 -25.0 1.014641 3 -25.0 25.0 25.0 1.014862 4 25.0 -25.0 -25.0 1.003686 5 25.0 -25.0 25.0 1.029287 6 25.0 25.0 -25.0 1.009610 7 25.0 25.0 25.0 1.010005 REL: 8 0.345432 8.129340 1.016168 rel = 0.339936 Number of iterations 3 Min cost was 0.345432 Number of FunctionCalls 255 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 13.710556 sec Parameters at optimum (transmm) 0.06677 0.12865 0.01474 Parameters at optimum (rotdeg) -0.25393 0.02348 0.04006 Final costs ---------------- Number of surface hits 253321 WM Intensity 10049.0169 +/- 1498.6660 Ctx Intensity 10914.7133 +/- 1715.0982 Pct Contrast 7.8364 +/- 16.7264 Cost 0.3454 RelCost 0.3442 Reg at min cost was 0.99999 0.00199 0.00301 -0.75542; -0.00208 -0.36274 0.93189 -16.20429; -0.00295 0.93189 0.36274 12.02586; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/007/register.dof6.dat, type = 14 Original Reg 0.99999 0.00135 0.00351 -0.83853; -0.00277 -0.36687 0.93027 -16.38543; -0.00255 0.93027 0.36687 11.93827; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00000 -0.00064 0.00050 -0.08311; -0.00069 -0.00413 -0.00162 -0.18114; 0.00040 -0.00162 0.00413 -0.08759; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.209608 Computing change in rh position Surface-RMS-Diff-mm 0.217165 0.106742 0.540730 mri_segreg done MinCost: 0.345432 10049.016864 10914.713340 7.836355 tkregister2_cmdl --mov bold/007/template.nii.gz --reg bold/007/register.dof6.dat --noedit --ltaout bold/007/register.dof6.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/007/template.nii.gz reg file bold/007/register.dof6.dat LoadVol 0 ZeroCRAS 0 7.4.1 Diagnostic Level -1 ---- Input registration matrix -------- 0.99999 0.00199 0.00301 -0.75542; -0.00208 -0.36274 0.93189 -16.20429; -0.00295 0.93189 0.36274 12.02586; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: This is an unsigined short. INFO: loading target /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/007/template.nii.gz INFO: This is an unsigined short. Tmov: -------------------- -2.00000 0.00000 0.00000 110.00000; 0.00000 0.00000 2.00000 -60.00000; 0.00000 -2.00000 0.00000 110.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99999 0.00199 0.00301 -0.75542; -0.00208 -0.36274 0.93189 -16.20429; -0.00295 0.93189 0.36274 12.02586; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = 20240801_dw204 RegMat --------------------------- 0.99999 0.00199 0.00301 -0.75542; -0.00208 -0.36274 0.93189 -16.20429; -0.00295 0.93189 0.36274 12.02586; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue Jun 17 12:59:58 EDT 2025 Ended at Tue Jun 17 13:00:53 EDT 2025 BBR-Run-Time-Sec 55 bbregister Done To check results, run: tkregisterfv --mov bold/007/template.nii.gz --reg bold/007/register.dof6.lta --surfs --sd /Volumes/umms-hillmera/asem_ptsd/DW204 Tue Jun 17 13:00:53 EDT 2025 register-sess completed 20240801_dw204 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -per-run -update ------------------------------------------------ /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 Tue Jun 17 13:00:53 EDT 2025 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/register.dof6.lta -ndil 1 -nerode 0 Tue Jun 17 13:00:54 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/fsfast/bin/mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/register.dof6.lta -ndil 1 -nerode 0 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_vol2vol --mov template.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/register.dof6.lta --inv --interp nearest --o masks/brain.nii.gz --targ /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: -0.03510 0.99892 -0.03050 0.64655; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01603; 0.00000 0.00000 0.00000 1.00000; movvol template.nii.gz targvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz outvol masks/brain.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1751122749 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: -0.03510 0.99906 0.02535 -8.51147; 0.99892 0.03430 0.03139 -0.93930; -0.03050 -0.02643 0.99919 0.22943; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: -0.03510 0.02535 -0.99906 225.67645; -0.03050 0.99919 0.02643 1.45277; -0.99892 -0.03139 0.03430 255.92276; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i masks/brain.nii.gz --o masks/brain.nii.gz --min 0.5 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i masks/brain.nii.gz --o masks/brain.nii.gz --min 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 1191876 values in range Counting number of voxels in first frame Found 1191875 voxels in final mask Writing output to masks/brain.nii.gz Count: 1191875 1191875.000000 11534336 10.333278 mri_binarize done Diliating 1 mri_binarize --i masks/brain.nii.gz --min 0.5 --dilate 1 --o masks/brain.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i masks/brain.nii.gz --min 0.5 --dilate 1 --o masks/brain.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 1191876 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 1420469 voxels in final mask Writing output to masks/brain.nii.gz Count: 1420469 1420469.000000 11534336 12.315135 mri_binarize done Started at Tue Jun 17 13:00:54 EDT 2025 Ended at Tue Jun 17 13:00:58 EDT 2025 Mkbrainmask-Run-Time-Sec 4 mkbrainmask Done mri_binarize --i masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o masks/brain.e3.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o masks/brain.e3.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 1420470 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 995610 voxels in final mask Writing output to masks/brain.e3.nii.gz Count: 995610 995610.000000 11534336 8.631706 mri_binarize done mkbrainmask -i 002/template.nii.gz -o 002/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/register.dof6.lta -ndil 1 -nerode 0 Tue Jun 17 13:01:02 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/fsfast/bin/mkbrainmask -i 002/template.nii.gz -o 002/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/register.dof6.lta -ndil 1 -nerode 0 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_vol2vol --mov 002/template.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/register.dof6.lta --inv --interp nearest --o 002/masks/brain.nii.gz --targ /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: -0.03510 0.99892 -0.03050 0.64655; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01603; 0.00000 0.00000 0.00000 1.00000; movvol 002/template.nii.gz targvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz outvol 002/masks/brain.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750252952 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: -0.03510 0.99906 0.02535 -8.51147; 0.99892 0.03430 0.03139 -0.93930; -0.03050 -0.02643 0.99919 0.22943; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: -0.03510 0.02535 -0.99906 225.67645; -0.03050 0.99919 0.02643 1.45277; -0.99892 -0.03139 0.03430 255.92276; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 002/masks/brain.nii.gz --o 002/masks/brain.nii.gz --min 0.5 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 002/masks/brain.nii.gz --o 002/masks/brain.nii.gz --min 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 002/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 002/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 1191876 values in range Counting number of voxels in first frame Found 1191875 voxels in final mask Writing output to 002/masks/brain.nii.gz Count: 1191875 1191875.000000 11534336 10.333278 mri_binarize done Diliating 1 mri_binarize --i 002/masks/brain.nii.gz --min 0.5 --dilate 1 --o 002/masks/brain.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 002/masks/brain.nii.gz --min 0.5 --dilate 1 --o 002/masks/brain.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 002/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 002/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 1191876 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 1420469 voxels in final mask Writing output to 002/masks/brain.nii.gz Count: 1420469 1420469.000000 11534336 12.315135 mri_binarize done Started at Tue Jun 17 13:01:02 EDT 2025 Ended at Tue Jun 17 13:01:06 EDT 2025 Mkbrainmask-Run-Time-Sec 4 mkbrainmask Done mri_binarize --i 002/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 002/masks/brain.e3.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 002/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 002/masks/brain.e3.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 002/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 002/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 1420470 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 995610 voxels in final mask Writing output to 002/masks/brain.e3.nii.gz Count: 995610 995610.000000 11534336 8.631706 mri_binarize done mkbrainmask -i 003/template.nii.gz -o 003/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/register.dof6.lta -ndil 1 -nerode 0 Tue Jun 17 13:01:10 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/fsfast/bin/mkbrainmask -i 003/template.nii.gz -o 003/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/register.dof6.lta -ndil 1 -nerode 0 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_vol2vol --mov 003/template.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/register.dof6.lta --inv --interp nearest --o 003/masks/brain.nii.gz --targ /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99995 -0.00300 0.00925 -0.46387; -0.00971 -0.35421 0.93512 -14.17781; -0.00047 0.93516 0.35422 10.90225; 0.00000 0.00000 0.00000 1.00000; movvol 003/template.nii.gz targvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz outvol 003/masks/brain.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1751013890 Invert! INFO: This is an unsigined short. Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99995 -0.00971 -0.00047 0.33130; -0.00300 -0.35421 0.93516 -15.21868; 0.00925 0.93512 0.35422 9.40035; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 1.99991 -0.00094 0.01942 17.10419; 0.01850 0.70845 -1.87023 138.46527; 0.00600 -1.87032 -0.70842 237.98851; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 003/masks/brain.nii.gz --o 003/masks/brain.nii.gz --min 0.5 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 003/masks/brain.nii.gz --o 003/masks/brain.nii.gz --min 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 003/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 003/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 148997 values in range Counting number of voxels in first frame Found 148996 voxels in final mask Writing output to 003/masks/brain.nii.gz Count: 148996 1191968.000000 774400 19.240186 mri_binarize done Diliating 1 mri_binarize --i 003/masks/brain.nii.gz --min 0.5 --dilate 1 --o 003/masks/brain.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 003/masks/brain.nii.gz --min 0.5 --dilate 1 --o 003/masks/brain.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 003/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 003/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 148997 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 193366 voxels in final mask Writing output to 003/masks/brain.nii.gz Count: 193366 1546928.000000 774400 24.969783 mri_binarize done Started at Tue Jun 17 13:01:10 EDT 2025 Ended at Tue Jun 17 13:01:11 EDT 2025 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i 003/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 003/masks/brain.e3.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 003/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 003/masks/brain.e3.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 003/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 003/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 192874 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 112838 voxels in final mask Writing output to 003/masks/brain.e3.nii.gz Count: 112838 902704.000000 774400 14.571023 mri_binarize done mkbrainmask -i 004/template.nii.gz -o 004/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/register.dof6.lta -ndil 1 -nerode 0 Tue Jun 17 13:01:12 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/fsfast/bin/mkbrainmask -i 004/template.nii.gz -o 004/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/register.dof6.lta -ndil 1 -nerode 0 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_vol2vol --mov 004/template.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/register.dof6.lta --inv --interp nearest --o 004/masks/brain.nii.gz --targ /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99988 0.00031 0.01560 -0.73120; -0.01437 -0.37068 0.92865 -13.70918; -0.00607 0.92876 0.37063 12.62407; 0.00000 0.00000 0.00000 1.00000; movvol 004/template.nii.gz targvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz outvol 004/masks/brain.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750718088 Invert! INFO: This is an unsigined short. Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99988 -0.01437 -0.00607 0.61069; 0.00031 -0.37068 0.92876 -16.80620; 0.01560 0.92865 0.37063 8.06364; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 1.99976 -0.01213 0.02874 17.15031; 0.03119 0.74125 -1.85730 136.88551; -0.00062 -1.85752 -0.74135 237.11481; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 004/masks/brain.nii.gz --o 004/masks/brain.nii.gz --min 0.5 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 004/masks/brain.nii.gz --o 004/masks/brain.nii.gz --min 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 004/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 004/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149028 values in range Counting number of voxels in first frame Found 149027 voxels in final mask Writing output to 004/masks/brain.nii.gz Count: 149027 1192216.000000 774400 19.244189 mri_binarize done Diliating 1 mri_binarize --i 004/masks/brain.nii.gz --min 0.5 --dilate 1 --o 004/masks/brain.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 004/masks/brain.nii.gz --min 0.5 --dilate 1 --o 004/masks/brain.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 004/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 004/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149028 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 193302 voxels in final mask Writing output to 004/masks/brain.nii.gz Count: 193302 1546416.000000 774400 24.961519 mri_binarize done Started at Tue Jun 17 13:01:12 EDT 2025 Ended at Tue Jun 17 13:01:13 EDT 2025 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i 004/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 004/masks/brain.e3.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 004/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 004/masks/brain.e3.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 004/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 004/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 192984 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 112518 voxels in final mask Writing output to 004/masks/brain.e3.nii.gz Count: 112518 900144.000000 774400 14.529700 mri_binarize done mkbrainmask -i 005/template.nii.gz -o 005/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/register.dof6.lta -ndil 1 -nerode 0 Tue Jun 17 13:01:13 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/fsfast/bin/mkbrainmask -i 005/template.nii.gz -o 005/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/register.dof6.lta -ndil 1 -nerode 0 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_vol2vol --mov 005/template.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/register.dof6.lta --inv --interp nearest --o 005/masks/brain.nii.gz --targ /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99994 0.00665 0.00842 -0.60532; -0.00548 -0.35819 0.93363 -16.52873; -0.00923 0.93363 0.35813 12.42867; 0.00000 0.00000 0.00000 1.00000; movvol 005/template.nii.gz targvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz outvol 005/masks/brain.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750340364 Invert! INFO: This is an unsigined short. Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99994 -0.00548 -0.00923 0.62940; 0.00665 -0.35819 0.93363 -17.52011; 0.00842 0.93363 0.35813 10.98576; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 1.99989 -0.01846 0.01096 18.06332; 0.01685 0.71626 -1.86727 132.71106; -0.01331 -1.86725 -0.71638 235.40204; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 005/masks/brain.nii.gz --o 005/masks/brain.nii.gz --min 0.5 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 005/masks/brain.nii.gz --o 005/masks/brain.nii.gz --min 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 005/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 005/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 147870 values in range Counting number of voxels in first frame Found 147869 voxels in final mask Writing output to 005/masks/brain.nii.gz Count: 147869 1182952.000000 726000 20.367631 mri_binarize done Diliating 1 mri_binarize --i 005/masks/brain.nii.gz --min 0.5 --dilate 1 --o 005/masks/brain.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 005/masks/brain.nii.gz --min 0.5 --dilate 1 --o 005/masks/brain.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 005/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 005/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 147870 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 190757 voxels in final mask Writing output to 005/masks/brain.nii.gz Count: 190757 1526056.000000 726000 26.275069 mri_binarize done Started at Tue Jun 17 13:01:13 EDT 2025 Ended at Tue Jun 17 13:01:14 EDT 2025 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i 005/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 005/masks/brain.e3.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 005/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 005/masks/brain.e3.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 005/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 005/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 189419 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 111364 voxels in final mask Writing output to 005/masks/brain.e3.nii.gz Count: 111364 890912.000000 726000 15.339394 mri_binarize done mkbrainmask -i 006/template.nii.gz -o 006/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/register.dof6.lta -ndil 1 -nerode 0 Tue Jun 17 13:01:15 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/fsfast/bin/mkbrainmask -i 006/template.nii.gz -o 006/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/register.dof6.lta -ndil 1 -nerode 0 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_vol2vol --mov 006/template.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/register.dof6.lta --inv --interp nearest --o 006/masks/brain.nii.gz --targ /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99990 0.00705 0.01226 -0.54247; -0.00863 -0.38302 0.92370 -16.86917; -0.01121 0.92371 0.38292 12.15179; 0.00000 0.00000 0.00000 1.00000; movvol 006/template.nii.gz targvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz outvol 006/masks/brain.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750910592 Invert! INFO: This is an unsigined short. Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99990 -0.00863 -0.01121 0.53316; 0.00705 -0.38302 0.92371 -17.68213; 0.01226 0.92370 0.38292 10.93560; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 1.99980 -0.02243 0.01725 18.19371; 0.02452 0.76583 -1.84740 129.01675; -0.01411 -1.84743 -0.76603 235.68344; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 006/masks/brain.nii.gz --o 006/masks/brain.nii.gz --min 0.5 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 006/masks/brain.nii.gz --o 006/masks/brain.nii.gz --min 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 006/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 006/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 148036 values in range Counting number of voxels in first frame Found 148035 voxels in final mask Writing output to 006/masks/brain.nii.gz Count: 148035 1184280.000000 726000 20.390496 mri_binarize done Diliating 1 mri_binarize --i 006/masks/brain.nii.gz --min 0.5 --dilate 1 --o 006/masks/brain.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 006/masks/brain.nii.gz --min 0.5 --dilate 1 --o 006/masks/brain.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 006/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 006/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 148036 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 191068 voxels in final mask Writing output to 006/masks/brain.nii.gz Count: 191068 1528544.000000 726000 26.317906 mri_binarize done Started at Tue Jun 17 13:01:15 EDT 2025 Ended at Tue Jun 17 13:01:16 EDT 2025 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i 006/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 006/masks/brain.e3.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 006/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 006/masks/brain.e3.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 006/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 006/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 189741 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 111378 voxels in final mask Writing output to 006/masks/brain.e3.nii.gz Count: 111378 891024.000000 726000 15.341322 mri_binarize done mkbrainmask -i 007/template.nii.gz -o 007/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/register.dof6.lta -ndil 1 -nerode 0 Tue Jun 17 13:01:17 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/fsfast/bin/mkbrainmask -i 007/template.nii.gz -o 007/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/register.dof6.lta -ndil 1 -nerode 0 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_vol2vol --mov 007/template.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/register.dof6.lta --inv --interp nearest --o 007/masks/brain.nii.gz --targ /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99999 0.00199 0.00301 -0.75541; -0.00208 -0.36274 0.93189 -16.20432; -0.00295 0.93189 0.36274 12.02583; 0.00000 0.00000 0.00000 1.00000; movvol 007/template.nii.gz targvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/mri/aparc+aseg.mgz outvol 007/masks/brain.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750500843 Invert! INFO: This is an unsigined short. Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99999 -0.00208 -0.00295 0.75712; 0.00199 -0.36274 0.93189 -17.08323; 0.00301 0.93189 0.36274 10.74062; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 1.99999 -0.00589 0.00416 17.44278; 0.00601 0.72548 -1.86377 132.94058; -0.00398 -1.86377 -0.72549 235.40788; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 007/masks/brain.nii.gz --o 007/masks/brain.nii.gz --min 0.5 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 007/masks/brain.nii.gz --o 007/masks/brain.nii.gz --min 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 007/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 007/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 148084 values in range Counting number of voxels in first frame Found 148083 voxels in final mask Writing output to 007/masks/brain.nii.gz Count: 148083 1184664.000000 726000 20.397107 mri_binarize done Diliating 1 mri_binarize --i 007/masks/brain.nii.gz --min 0.5 --dilate 1 --o 007/masks/brain.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 007/masks/brain.nii.gz --min 0.5 --dilate 1 --o 007/masks/brain.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 007/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 007/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 148084 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 191043 voxels in final mask Writing output to 007/masks/brain.nii.gz Count: 191043 1528344.000000 726000 26.314463 mri_binarize done Started at Tue Jun 17 13:01:17 EDT 2025 Ended at Tue Jun 17 13:01:18 EDT 2025 Mkbrainmask-Run-Time-Sec 0 mkbrainmask Done mri_binarize --i 007/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 007/masks/brain.e3.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_binarize --i 007/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 007/masks/brain.e3.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 007/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 007/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 189736 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 111493 voxels in final mask Writing output to 007/masks/brain.e3.nii.gz Count: 111493 891944.000000 726000 15.357163 mri_binarize done meanval --i 002/f.nii --m 002/masks/brain.e3.nii.gz --o 002/global.meanval.dat --avgwf 002/global.waveform.dat Tue Jun 17 13:01:18 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/bin/meanval --i 002/f.nii --m 002/masks/brain.e3.nii.gz --o 002/global.meanval.dat --avgwf 002/global.waveform.dat freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_segstats --seg 002/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmpdir.meanval.91857/blah.91857 --in 002/f.nii --sfavg 002/global.meanval.dat --avgwf 002/global.waveform.dat 7.4.1 cwd cmdline mri_segstats --seg 002/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmpdir.meanval.91857/blah.91857 --in 002/f.nii --sfavg 002/global.meanval.dat --avgwf 002/global.waveform.dat sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch whitesurfname white UseRobust 0 Loading 002/masks/brain.e3.nii.gz Loading 002/f.nii Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to 002/global.meanval.dat 0 338.209 Writing to 002/global.waveform.dat mri_segstats done meanval --i 003/f.nii --m 003/masks/brain.e3.nii.gz --o 003/global.meanval.dat --avgwf 003/global.waveform.dat Tue Jun 17 13:01:21 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/bin/meanval --i 003/f.nii --m 003/masks/brain.e3.nii.gz --o 003/global.meanval.dat --avgwf 003/global.waveform.dat freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_segstats --seg 003/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmpdir.meanval.91907/blah.91907 --in 003/f.nii --sfavg 003/global.meanval.dat --avgwf 003/global.waveform.dat 7.4.1 cwd cmdline mri_segstats --seg 003/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmpdir.meanval.91907/blah.91907 --in 003/f.nii --sfavg 003/global.meanval.dat --avgwf 003/global.waveform.dat sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch whitesurfname white UseRobust 0 Loading 003/masks/brain.e3.nii.gz Loading 003/f.nii INFO: This is an unsigined short. Voxel Volume is 8 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to 003/global.meanval.dat 0 1414.06 Writing to 003/global.waveform.dat mri_segstats done meanval --i 004/f.nii --m 004/masks/brain.e3.nii.gz --o 004/global.meanval.dat --avgwf 004/global.waveform.dat Tue Jun 17 13:01:23 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/bin/meanval --i 004/f.nii --m 004/masks/brain.e3.nii.gz --o 004/global.meanval.dat --avgwf 004/global.waveform.dat freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_segstats --seg 004/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmpdir.meanval.91957/blah.91957 --in 004/f.nii --sfavg 004/global.meanval.dat --avgwf 004/global.waveform.dat 7.4.1 cwd cmdline mri_segstats --seg 004/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmpdir.meanval.91957/blah.91957 --in 004/f.nii --sfavg 004/global.meanval.dat --avgwf 004/global.waveform.dat sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch whitesurfname white UseRobust 0 Loading 004/masks/brain.e3.nii.gz Loading 004/f.nii INFO: This is an unsigined short. Voxel Volume is 8 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to 004/global.meanval.dat 0 1434.18 Writing to 004/global.waveform.dat mri_segstats done meanval --i 005/f.nii --m 005/masks/brain.e3.nii.gz --o 005/global.meanval.dat --avgwf 005/global.waveform.dat Tue Jun 17 13:01:26 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/bin/meanval --i 005/f.nii --m 005/masks/brain.e3.nii.gz --o 005/global.meanval.dat --avgwf 005/global.waveform.dat freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_segstats --seg 005/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmpdir.meanval.92007/blah.92007 --in 005/f.nii --sfavg 005/global.meanval.dat --avgwf 005/global.waveform.dat 7.4.1 cwd cmdline mri_segstats --seg 005/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmpdir.meanval.92007/blah.92007 --in 005/f.nii --sfavg 005/global.meanval.dat --avgwf 005/global.waveform.dat sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch whitesurfname white UseRobust 0 Loading 005/masks/brain.e3.nii.gz Loading 005/f.nii INFO: This is an unsigined short. Voxel Volume is 8 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to 005/global.meanval.dat 0 10883.9 Writing to 005/global.waveform.dat mri_segstats done meanval --i 006/f.nii --m 006/masks/brain.e3.nii.gz --o 006/global.meanval.dat --avgwf 006/global.waveform.dat Tue Jun 17 13:01:47 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/bin/meanval --i 006/f.nii --m 006/masks/brain.e3.nii.gz --o 006/global.meanval.dat --avgwf 006/global.waveform.dat freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_segstats --seg 006/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmpdir.meanval.92057/blah.92057 --in 006/f.nii --sfavg 006/global.meanval.dat --avgwf 006/global.waveform.dat 7.4.1 cwd cmdline mri_segstats --seg 006/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmpdir.meanval.92057/blah.92057 --in 006/f.nii --sfavg 006/global.meanval.dat --avgwf 006/global.waveform.dat sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch whitesurfname white UseRobust 0 Loading 006/masks/brain.e3.nii.gz Loading 006/f.nii INFO: This is an unsigined short. Voxel Volume is 8 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to 006/global.meanval.dat 0 10925 Writing to 006/global.waveform.dat mri_segstats done meanval --i 007/f.nii --m 007/masks/brain.e3.nii.gz --o 007/global.meanval.dat --avgwf 007/global.waveform.dat Tue Jun 17 13:02:13 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/bin/meanval --i 007/f.nii --m 007/masks/brain.e3.nii.gz --o 007/global.meanval.dat --avgwf 007/global.waveform.dat freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_segstats --seg 007/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmpdir.meanval.92107/blah.92107 --in 007/f.nii --sfavg 007/global.meanval.dat --avgwf 007/global.waveform.dat 7.4.1 cwd cmdline mri_segstats --seg 007/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmpdir.meanval.92107/blah.92107 --in 007/f.nii --sfavg 007/global.meanval.dat --avgwf 007/global.waveform.dat sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch whitesurfname white UseRobust 0 Loading 007/masks/brain.e3.nii.gz Loading 007/f.nii INFO: This is an unsigined short. Voxel Volume is 8 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to 007/global.meanval.dat 0 10848.4 Writing to 007/global.waveform.dat mri_segstats done Tue Jun 17 13:02:20 EDT 2025 mkbrainmask-sess done 20240801_dw204 MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -per-run -update Logfile is /Volumes/umms-hillmera/asem_ptsd/DW204/log/mc-20240801_dw204-bold.log ------------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 RunList: 002 003 004 005 006 007 ------- ************************** ----------- ------- Motion Correcting Run 002 ----------- ------- ************************** ----------- sess = 20240801_dw204 Tue Jun 17 13:02:21 EDT 2025 mc-afni2 --i 002/f.nii --t 002/template.nii.gz --o 002/fmcpr.nii.gz --mcdat 002/fmcpr.mcdat /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_info --nframes --o /tmp/mriinfo.92244 002/template.nii.gz log file is 002/fmcpr.nii.gz.mclog mcdat file is 002/fmcpr.mcdat tmp dir is 002/tmp.mc-afni2.92244 #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 002/template.nii.gz 002/tmp.mc-afni2.92244/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 002/template.nii.gz 002/tmp.mc-afni2.92244/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 reading from 002/template.nii.gz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) changing data type from short to float (noscale = 0)... writing to 002/tmp.mc-afni2.92244/tempvol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 002/f.nii 002/tmp.mc-afni2.92244/invol.nii.gz -odt float mri_convert 002/f.nii 002/tmp.mc-afni2.92244/invol.nii.gz -odt float reading from 002/f.nii... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) changing data type from short to float (noscale = 0)... writing to 002/tmp.mc-afni2.92244/invol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold 3dvolreg.afni -verbose -dfile 002/fmcpr.mcdat -1Dmatrix_save 002/fmcpr.mat -base 002/tmp.mc-afni2.92244/tempvol.nii.gz -prefix 002/tmp.mc-afni2.92244/outvol.nii.gz 002/tmp.mc-afni2.92244/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (May 22 2013) [64-bit] ++ Authored by: RW Cox ++ Reading in base dataset 002/tmp.mc-afni2.92244/tempvol.nii.gz ++ Reading input dataset 002/tmp.mc-afni2.92244/invol.nii.gz ++ Edging: x=13 y=13 z=9 ++ Creating mask for -maxdisp + Automask has 4781390 voxels + 135886 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 1 sub-bricks: 0.. ++ CPU time for realignment=0.09 s ++ Min : roll=+0.000 pitch=-0.000 yaw=+0.000 dS=-0.000 dL=-0.000 dP=+0.000 ++ Mean: roll=+0.000 pitch=-0.000 yaw=+0.000 dS=-0.000 dL=-0.000 dP=+0.000 ++ Max : roll=+0.000 pitch=-0.000 yaw=+0.000 dS=-0.000 dL=-0.000 dP=+0.000 ++ Max displacements (mm) for each sub-brick: 0.00 ++ Max displacement in automask = 0.00 (mm) at sub-brick 0 ++ Wrote dataset to disk in 002/tmp.mc-afni2.92244/outvol.nii.gz #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 002/tmp.mc-afni2.92244/outvol.nii.gz 002/fmcpr.nii.gz --in_like 002/template.nii.gz mri_convert 002/tmp.mc-afni2.92244/outvol.nii.gz 002/fmcpr.nii.gz --in_like 002/template.nii.gz reading info from 002/template.nii.gz... reading from 002/tmp.mc-afni2.92244/outvol.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to 002/fmcpr.nii.gz... ... cleaning up .... Tue Jun 17 13:02:43 EDT 2025 mc-afni2 done INFO: Making external regressor from mc params mcdat2mcextreg --i 002/fmcpr.mcdat --o 002/mcprextreg Tue Jun 17 13:02:43 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/fsfast/bin/mcdat2mcextreg --i 002/fmcpr.mcdat --o 002/mcprextreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmpdir.mcdat2extreg.92342/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmpdir.mcdat2extreg.92342/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmpdir.mcdat2extreg.92342/y.out.nii --pca 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmpdir.mcdat2extreg.92342/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmpdir.mcdat2extreg.92342/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmpdir.mcdat2extreg.92342/y.out.nii --pca sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmpdir.mcdat2extreg.92342/table.dat logyflag 0 usedti 0 glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmpdir.mcdat2extreg.92342/glm IllCondOK 0 ReScaleX 1 DoFFx 0 SigUseDouble 1 Creating output directory /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmpdir.mcdat2extreg.92342/glm Loading y from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmpdir.mcdat2extreg.92342/table.dat Found 6 data colums Found 1 data rows Saving design matrix to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmpdir.mcdat2extreg.92342/glm/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 0 ERROR: DOF = 0 (base) hibahmch@mac-mvqmt7cvdq DW204 % preproc-sess -s 20240801_dw204 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.20240801_dw204.log -------------------------------------------------------------- FreeSurferEnv.csh 7.4.1 hibahmch setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 /Volumes/umms-hillmera/asem_ptsd/DW204 /Applications/freesurfer/fsfast/bin/preproc-sess -s 20240801_dw204 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Tue Jun 17 14:00:48 EDT 2025 instem f mc 1 f fmcpr stc 1 fmcpr fmcpr.up sm 0 mask 1 brain 20240801_dw204 Template ----------------------------- mktemplate-sess -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -funcstem f -update Session: /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 ---------------- Tue Jun 17 14:00:49 EDT 2025 Detected input format at nii 20240801_dw204 Update not needed Run: 002 ---------------- Tue Jun 17 14:00:49 EDT 2025 20240801_dw204 002 Update not needed Run: 003 ---------------- Tue Jun 17 14:00:49 EDT 2025 20240801_dw204 003 Update not needed Run: 004 ---------------- Tue Jun 17 14:00:49 EDT 2025 20240801_dw204 004 Update not needed Run: 005 ---------------- Tue Jun 17 14:00:49 EDT 2025 20240801_dw204 005 Update not needed Run: 006 ---------------- Tue Jun 17 14:00:50 EDT 2025 20240801_dw204 006 Update not needed Run: 007 ---------------- Tue Jun 17 14:00:50 EDT 2025 20240801_dw204 007 Update not needed Tue Jun 17 14:00:50 EDT 2025 mktemplate-sess completed 20240801_dw204 Registration ----------------------------- register-sess -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg -------------------------------------------------------------- register-sess logfile is /Volumes/umms-hillmera/asem_ptsd/DW204/log/register-sess.20240801_dw204.log -------------------------------------------------------------- Tue Jun 17 14:00:50 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204 /Applications/freesurfer/fsfast/bin/register-sess -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 Session: /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 ---------------- Tue Jun 17 14:00:50 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 Run: 002 ---------------- Tue Jun 17 14:00:51 EDT 2025 Update not needed Run: 003 ---------------- Tue Jun 17 14:00:51 EDT 2025 Update not needed Run: 004 ---------------- Tue Jun 17 14:00:51 EDT 2025 Update not needed Run: 005 ---------------- Tue Jun 17 14:00:51 EDT 2025 Update not needed Run: 006 ---------------- Tue Jun 17 14:00:51 EDT 2025 Update not needed Run: 007 ---------------- Tue Jun 17 14:00:51 EDT 2025 Update not needed Tue Jun 17 14:00:51 EDT 2025 register-sess completed 20240801_dw204 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -per-run -update ------------------------------------------------ /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 Tue Jun 17 14:00:51 EDT 2025 20240801_dw204 Update not needed for session-level mask 20240801_dw204 Update not needed for run 002 mask 20240801_dw204 Update not needed for run 003 mask 20240801_dw204 Update not needed for run 004 mask 20240801_dw204 Update not needed for run 005 mask 20240801_dw204 Update not needed for run 006 mask 20240801_dw204 Update not needed for run 007 mask 20240801_dw204 Update not needed for run 002 meanval 20240801_dw204 Update not needed for run 003 meanval 20240801_dw204 Update not needed for run 004 meanval 20240801_dw204 Update not needed for run 005 meanval 20240801_dw204 Update not needed for run 006 meanval 20240801_dw204 Update not needed for run 007 meanval Tue Jun 17 14:00:53 EDT 2025 mkbrainmask-sess done 20240801_dw204 MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -per-run -update Logfile is /Volumes/umms-hillmera/asem_ptsd/DW204/log/mc-20240801_dw204-bold.log ------------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204 RunList: 002 003 004 005 006 007 20240801_dw204 002 Update not needed ------- ************************** ----------- ------- Motion Correcting Run 003 ----------- ------- ************************** ----------- sess = 20240801_dw204 Tue Jun 17 14:00:54 EDT 2025 mc-afni2 --i 003/f.nii --t 003/template.nii.gz --o 003/fmcpr.nii.gz --mcdat 003/fmcpr.mcdat /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_info --nframes --o /tmp/mriinfo.94341 003/template.nii.gz INFO: This is an unsigined short. log file is 003/fmcpr.nii.gz.mclog mcdat file is 003/fmcpr.mcdat tmp dir is 003/tmp.mc-afni2.94341 #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 003/template.nii.gz 003/tmp.mc-afni2.94341/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 003/template.nii.gz 003/tmp.mc-afni2.94341/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 reading from 003/template.nii.gz... INFO: This is an unsigined short. TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) changing data type from ushrt to float (noscale = 0)... writing to 003/tmp.mc-afni2.94341/tempvol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 003/f.nii 003/tmp.mc-afni2.94341/invol.nii.gz -odt float mri_convert 003/f.nii 003/tmp.mc-afni2.94341/invol.nii.gz -odt float reading from 003/f.nii... INFO: This is an unsigined short. TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) changing data type from ushrt to float (noscale = 0)... writing to 003/tmp.mc-afni2.94341/invol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold 3dvolreg.afni -verbose -dfile 003/fmcpr.mcdat -1Dmatrix_save 003/fmcpr.mat -base 003/tmp.mc-afni2.94341/tempvol.nii.gz -prefix 003/tmp.mc-afni2.94341/outvol.nii.gz 003/tmp.mc-afni2.94341/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (May 22 2013) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 003/tmp.mc-afni2.94341/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:003/tmp.mc-afni2.94341/tempvol.nii.gz is 21.899994 degrees from plumb. ++ Reading in base dataset 003/tmp.mc-afni2.94341/tempvol.nii.gz ++ Oblique dataset:003/tmp.mc-afni2.94341/invol.nii.gz is 21.899994 degrees from plumb. ++ Reading input dataset 003/tmp.mc-afni2.94341/invol.nii.gz ++ Edging: x=6 y=6 z=3 ++ Creating mask for -maxdisp + Automask has 766052 voxels + 50757 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 65 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64.. ++ CPU time for realignment=3.46 s [=0.0532 s/sub-brick] ++ Min : roll=-0.034 pitch=-0.565 yaw=-0.180 dS=-4.398 dL=-0.099 dP=-0.203 ++ Mean: roll=+0.012 pitch=+0.013 yaw=-0.025 dS=-0.115 dL=-0.004 dP=+0.035 ++ Max : roll=+0.137 pitch=+0.263 yaw=+0.042 dS=+0.047 dL=+0.040 dP=+3.043 ++ Max displacements (mm) for each sub-brick: 6.76 0.32 0.32 0.28 0.34 0.52 0.95 0.70 0.64 0.62 0.66 0.50 0.52 0.38 0.42 0.27 0.32 0.24 0.23 0.34 0.27 0.25 0.18 0.23 0.20 0.05 0.22 0.22 0.09 0.10 0.21 0.14 0.00 0.08 0.03 0.12 0.16 0.23 0.14 0.12 0.09 0.14 0.11 0.13 0.11 0.13 0.12 0.19 0.26 0.19 0.17 0.22 0.18 0.25 0.28 0.17 0.18 0.21 0.23 0.28 0.34 0.40 0.29 0.40 0.36 ++ Max displacement in automask = 6.76 (mm) at sub-brick 0 ++ Wrote dataset to disk in 003/tmp.mc-afni2.94341/outvol.nii.gz #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 003/tmp.mc-afni2.94341/outvol.nii.gz 003/fmcpr.nii.gz --in_like 003/template.nii.gz mri_convert 003/tmp.mc-afni2.94341/outvol.nii.gz 003/fmcpr.nii.gz --in_like 003/template.nii.gz reading info from 003/template.nii.gz... INFO: This is an unsigined short. reading from 003/tmp.mc-afni2.94341/outvol.nii.gz... TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 INFO: frames are not the same i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) writing to 003/fmcpr.nii.gz... ... cleaning up .... Tue Jun 17 14:01:53 EDT 2025 mc-afni2 done INFO: Making external regressor from mc params mcdat2mcextreg --i 003/fmcpr.mcdat --o 003/mcprextreg Tue Jun 17 14:01:53 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/fsfast/bin/mcdat2mcextreg --i 003/fmcpr.mcdat --o 003/mcprextreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmpdir.mcdat2extreg.94440/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmpdir.mcdat2extreg.94440/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmpdir.mcdat2extreg.94440/y.out.nii --pca 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmpdir.mcdat2extreg.94440/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmpdir.mcdat2extreg.94440/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmpdir.mcdat2extreg.94440/y.out.nii --pca sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmpdir.mcdat2extreg.94440/table.dat logyflag 0 usedti 0 glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmpdir.mcdat2extreg.94440/glm IllCondOK 0 ReScaleX 1 DoFFx 0 SigUseDouble 1 Creating output directory /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmpdir.mcdat2extreg.94440/glm Loading y from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmpdir.mcdat2extreg.94440/table.dat Found 6 data colums Found 65 data rows Saving design matrix to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmpdir.mcdat2extreg.94440/glm/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 64 Starting fit and test Fit completed in 1.66667e-05 minutes Writing results osgm maxvox sig=-5.30075 F=24.8482 at index 2 0 0 seed=1751031769 Computing efficiency Measure:MC osgm Tx 3.386 Ty 0.519 Tz 5.301 Rx 1.033 Ry 0.578 Rz 0.326 Computing PCA (65) mri_glmfit done ninputs = 1 Checking inputs nframestot = 65 Allocing output Done allocing nframes = 65 Computing PCA Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmpdir.mcdat2extreg.94440/pca.nii mcdat2mcextreg done ------- ************************** ----------- ------- Motion Correcting Run 004 ----------- ------- ************************** ----------- sess = 20240801_dw204 Tue Jun 17 14:01:54 EDT 2025 mc-afni2 --i 004/f.nii --t 004/template.nii.gz --o 004/fmcpr.nii.gz --mcdat 004/fmcpr.mcdat /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_info --nframes --o /tmp/mriinfo.94504 004/template.nii.gz INFO: This is an unsigined short. log file is 004/fmcpr.nii.gz.mclog mcdat file is 004/fmcpr.mcdat tmp dir is 004/tmp.mc-afni2.94504 #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 004/template.nii.gz 004/tmp.mc-afni2.94504/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 004/template.nii.gz 004/tmp.mc-afni2.94504/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 reading from 004/template.nii.gz... INFO: This is an unsigined short. TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) changing data type from ushrt to float (noscale = 0)... writing to 004/tmp.mc-afni2.94504/tempvol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 004/f.nii 004/tmp.mc-afni2.94504/invol.nii.gz -odt float mri_convert 004/f.nii 004/tmp.mc-afni2.94504/invol.nii.gz -odt float reading from 004/f.nii... INFO: This is an unsigined short. TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) changing data type from ushrt to float (noscale = 0)... writing to 004/tmp.mc-afni2.94504/invol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save 004/fmcpr.mat -base 004/tmp.mc-afni2.94504/tempvol.nii.gz -prefix 004/tmp.mc-afni2.94504/outvol.nii.gz 004/tmp.mc-afni2.94504/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (May 22 2013) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 004/tmp.mc-afni2.94504/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:004/tmp.mc-afni2.94504/tempvol.nii.gz is 21.899994 degrees from plumb. ++ Reading in base dataset 004/tmp.mc-afni2.94504/tempvol.nii.gz ++ Oblique dataset:004/tmp.mc-afni2.94504/invol.nii.gz is 21.899994 degrees from plumb. ++ Reading input dataset 004/tmp.mc-afni2.94504/invol.nii.gz ++ Edging: x=6 y=6 z=3 ++ Creating mask for -maxdisp + Automask has 764500 voxels + 50620 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 65 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64.. ++ CPU time for realignment=3.62 s [=0.0557 s/sub-brick] ++ Min : roll=-0.279 pitch=-0.034 yaw=-0.727 dS=-4.093 dL=-0.199 dP=-0.278 ++ Mean: roll=+0.006 pitch=+0.060 yaw=+0.007 dS=-0.052 dL=-0.015 dP=-0.031 ++ Max : roll=+0.060 pitch=+0.476 yaw=+0.083 dS=+0.108 dL=+0.011 dP=+1.107 ++ Max displacements (mm) for each sub-brick: 6.72 1.51 1.36 0.96 0.61 0.42 0.27 0.37 0.29 0.35 0.26 0.24 0.30 0.14 0.26 0.32 0.19 0.34 0.18 0.25 0.25 0.18 0.25 0.17 0.26 0.20 0.14 0.21 0.13 0.13 0.18 0.17 0.00 0.30 0.04 0.07 0.13 0.17 0.12 0.20 0.08 0.28 0.18 0.11 0.20 0.17 0.26 0.12 0.18 0.19 0.13 0.26 0.24 0.16 0.48 0.25 0.34 0.20 0.36 0.24 0.33 0.28 0.38 0.24 0.37 ++ Max displacement in automask = 6.72 (mm) at sub-brick 0 ++ Wrote dataset to disk in 004/tmp.mc-afni2.94504/outvol.nii.gz #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 004/tmp.mc-afni2.94504/outvol.nii.gz 004/fmcpr.nii.gz --in_like 004/template.nii.gz mri_convert 004/tmp.mc-afni2.94504/outvol.nii.gz 004/fmcpr.nii.gz --in_like 004/template.nii.gz reading info from 004/template.nii.gz... INFO: This is an unsigined short. reading from 004/tmp.mc-afni2.94504/outvol.nii.gz... TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 INFO: frames are not the same i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) writing to 004/fmcpr.nii.gz... ... cleaning up .... Tue Jun 17 14:02:37 EDT 2025 mc-afni2 done INFO: Making external regressor from mc params mcdat2mcextreg --i 004/fmcpr.mcdat --o 004/mcprextreg Tue Jun 17 14:02:37 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/fsfast/bin/mcdat2mcextreg --i 004/fmcpr.mcdat --o 004/mcprextreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmpdir.mcdat2extreg.94603/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmpdir.mcdat2extreg.94603/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmpdir.mcdat2extreg.94603/y.out.nii --pca 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmpdir.mcdat2extreg.94603/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmpdir.mcdat2extreg.94603/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmpdir.mcdat2extreg.94603/y.out.nii --pca sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmpdir.mcdat2extreg.94603/table.dat logyflag 0 usedti 0 glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmpdir.mcdat2extreg.94603/glm IllCondOK 0 ReScaleX 1 DoFFx 0 SigUseDouble 1 Creating output directory /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmpdir.mcdat2extreg.94603/glm Loading y from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmpdir.mcdat2extreg.94603/table.dat Found 6 data colums Found 65 data rows Saving design matrix to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmpdir.mcdat2extreg.94603/glm/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 64 Starting fit and test Fit completed in 0 minutes Writing results osgm maxvox sig=5.09207 F=23.5715 at index 1 0 0 seed=1750883271 Computing efficiency Measure:MC osgm Tx 0.606 Ty 5.092 Tz 0.233 Rx 0.379 Ry 3.785 Rz 0.793 Computing PCA (65) mri_glmfit done ninputs = 1 Checking inputs nframestot = 65 Allocing output Done allocing nframes = 65 Computing PCA Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmpdir.mcdat2extreg.94603/pca.nii mcdat2mcextreg done ------- ************************** ----------- ------- Motion Correcting Run 005 ----------- ------- ************************** ----------- sess = 20240801_dw204 Tue Jun 17 14:02:38 EDT 2025 mc-afni2 --i 005/f.nii --t 005/template.nii.gz --o 005/fmcpr.nii.gz --mcdat 005/fmcpr.mcdat /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_info --nframes --o /tmp/mriinfo.94668 005/template.nii.gz INFO: This is an unsigined short. log file is 005/fmcpr.nii.gz.mclog mcdat file is 005/fmcpr.mcdat tmp dir is 005/tmp.mc-afni2.94668 #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 005/template.nii.gz 005/tmp.mc-afni2.94668/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 005/template.nii.gz 005/tmp.mc-afni2.94668/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 reading from 005/template.nii.gz... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) changing data type from ushrt to float (noscale = 0)... writing to 005/tmp.mc-afni2.94668/tempvol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 005/f.nii 005/tmp.mc-afni2.94668/invol.nii.gz -odt float mri_convert 005/f.nii 005/tmp.mc-afni2.94668/invol.nii.gz -odt float reading from 005/f.nii... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) changing data type from ushrt to float (noscale = 0)... writing to 005/tmp.mc-afni2.94668/invol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold 3dvolreg.afni -verbose -dfile 005/fmcpr.mcdat -1Dmatrix_save 005/fmcpr.mat -base 005/tmp.mc-afni2.94668/tempvol.nii.gz -prefix 005/tmp.mc-afni2.94668/outvol.nii.gz 005/tmp.mc-afni2.94668/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (May 22 2013) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 005/tmp.mc-afni2.94668/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:005/tmp.mc-afni2.94668/tempvol.nii.gz is 21.899994 degrees from plumb. ++ Reading in base dataset 005/tmp.mc-afni2.94668/tempvol.nii.gz ++ Oblique dataset:005/tmp.mc-afni2.94668/invol.nii.gz is 21.899994 degrees from plumb. ++ Reading input dataset 005/tmp.mc-afni2.94668/invol.nii.gz ++ Edging: x=6 y=6 z=3 ++ Creating mask for -maxdisp + Automask has 196168 voxels + 17793 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 100 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99.. ++ CPU time for realignment=4.68 s [=0.0468 s/sub-brick] ++ Min : roll=-0.007 pitch=-0.100 yaw=-0.042 dS=-0.102 dL=-0.009 dP=-0.036 ++ Mean: roll=+0.018 pitch=-0.045 yaw=-0.016 dS=-0.034 dL=+0.005 dP=+0.036 ++ Max : roll=+0.052 pitch=+0.022 yaw=+0.007 dS=+0.020 dL=+0.025 dP=+0.150 ++ Max displacements (mm) for each sub-brick: 0.15 0.13 0.17 0.17 0.19 0.14 0.12 0.10 0.17 0.13 0.13 0.11 0.10 0.16 0.17 0.18 0.14 0.13 0.17 0.17 0.13 0.09 0.15 0.18 0.16 0.13 0.09 0.10 0.19 0.18 0.15 0.10 0.11 0.16 0.13 0.10 0.09 0.16 0.14 0.12 0.08 0.13 0.22 0.24 0.24 0.16 0.09 0.15 0.11 0.04 0.00 0.04 0.12 0.11 0.11 0.07 0.13 0.16 0.14 0.07 0.15 0.18 0.12 0.08 0.06 0.05 0.07 0.14 0.22 0.20 0.15 0.11 0.19 0.21 0.14 0.08 0.16 0.19 0.15 0.11 0.13 0.20 0.16 0.11 0.12 0.22 0.17 0.11 0.10 0.18 0.17 0.14 0.15 0.20 0.16 0.13 0.22 0.20 0.15 0.12 ++ Max displacement in automask = 0.24 (mm) at sub-brick 43 ++ Wrote dataset to disk in 005/tmp.mc-afni2.94668/outvol.nii.gz #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 005/tmp.mc-afni2.94668/outvol.nii.gz 005/fmcpr.nii.gz --in_like 005/template.nii.gz mri_convert 005/tmp.mc-afni2.94668/outvol.nii.gz 005/fmcpr.nii.gz --in_like 005/template.nii.gz reading info from 005/template.nii.gz... INFO: This is an unsigined short. reading from 005/tmp.mc-afni2.94668/outvol.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 INFO: frames are not the same i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) writing to 005/fmcpr.nii.gz... ... cleaning up .... Tue Jun 17 14:03:42 EDT 2025 mc-afni2 done INFO: Making external regressor from mc params mcdat2mcextreg --i 005/fmcpr.mcdat --o 005/mcprextreg Tue Jun 17 14:03:42 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/fsfast/bin/mcdat2mcextreg --i 005/fmcpr.mcdat --o 005/mcprextreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmpdir.mcdat2extreg.94771/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmpdir.mcdat2extreg.94771/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmpdir.mcdat2extreg.94771/y.out.nii --pca 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmpdir.mcdat2extreg.94771/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmpdir.mcdat2extreg.94771/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmpdir.mcdat2extreg.94771/y.out.nii --pca sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmpdir.mcdat2extreg.94771/table.dat logyflag 0 usedti 0 glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmpdir.mcdat2extreg.94771/glm IllCondOK 0 ReScaleX 1 DoFFx 0 SigUseDouble 1 Creating output directory /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmpdir.mcdat2extreg.94771/glm Loading y from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmpdir.mcdat2extreg.94771/table.dat Found 6 data colums Found 100 data rows Saving design matrix to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmpdir.mcdat2extreg.94771/glm/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 99 Starting fit and test Fit completed in 0 minutes Writing results osgm maxvox sig=-34.1129 F=361.956 at index 1 0 0 seed=1750909437 Computing efficiency Measure:MC osgm Tx 17.334 Ty 34.113 Tz 20.672 Rx 23.680 Ry 6.636 Rz 13.569 Computing PCA (100) mri_glmfit done ninputs = 1 Checking inputs nframestot = 100 Allocing output Done allocing nframes = 100 Computing PCA Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmpdir.mcdat2extreg.94771/pca.nii mcdat2mcextreg done ------- ************************** ----------- ------- Motion Correcting Run 006 ----------- ------- ************************** ----------- sess = 20240801_dw204 Tue Jun 17 14:03:43 EDT 2025 mc-afni2 --i 006/f.nii --t 006/template.nii.gz --o 006/fmcpr.nii.gz --mcdat 006/fmcpr.mcdat /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_info --nframes --o /tmp/mriinfo.94835 006/template.nii.gz INFO: This is an unsigined short. log file is 006/fmcpr.nii.gz.mclog mcdat file is 006/fmcpr.mcdat tmp dir is 006/tmp.mc-afni2.94835 #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 006/template.nii.gz 006/tmp.mc-afni2.94835/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 006/template.nii.gz 006/tmp.mc-afni2.94835/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 reading from 006/template.nii.gz... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) changing data type from ushrt to float (noscale = 0)... writing to 006/tmp.mc-afni2.94835/tempvol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 006/f.nii 006/tmp.mc-afni2.94835/invol.nii.gz -odt float mri_convert 006/f.nii 006/tmp.mc-afni2.94835/invol.nii.gz -odt float reading from 006/f.nii... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) changing data type from ushrt to float (noscale = 0)... writing to 006/tmp.mc-afni2.94835/invol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold 3dvolreg.afni -verbose -dfile 006/fmcpr.mcdat -1Dmatrix_save 006/fmcpr.mat -base 006/tmp.mc-afni2.94835/tempvol.nii.gz -prefix 006/tmp.mc-afni2.94835/outvol.nii.gz 006/tmp.mc-afni2.94835/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (May 22 2013) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 006/tmp.mc-afni2.94835/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:006/tmp.mc-afni2.94835/tempvol.nii.gz is 21.899994 degrees from plumb. ++ Reading in base dataset 006/tmp.mc-afni2.94835/tempvol.nii.gz ++ Oblique dataset:006/tmp.mc-afni2.94835/invol.nii.gz is 21.899994 degrees from plumb. ++ Reading input dataset 006/tmp.mc-afni2.94835/invol.nii.gz ++ Edging: x=6 y=6 z=3 ++ Creating mask for -maxdisp + Automask has 197567 voxels + 17855 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 1212 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237..238..239..240..241..242..243..244..245..246..247..248..249..250..251..252..253..254..255..256..257..258..259..260..261..262..263..264..265..266..267..268..269..270..271..272..273..274..275..276..277..278..279..280..281..282..283..284..285..286..287..288..289..290..291..292..293..294..295..296..297..298..299..300..301..302..303..304..305..306..307..308..309..310..311..312..313..314..315..316..317..318..319..320..321..322..323..324..325..326..327..328..329..330..331..332..333..334..335..336..337..338..339..340..341..342..343..344..345..346..347..348..349..350..351..352..353..354..355..356..357..358..359..360..361..362..363..364..365..366..367..368..369..370..371..372..373..374..375..376..377..378..379..380..381..382..383..384..385..386..387..388..389..390..391..392..393..394..395..396..397..398..399..400..401..402..403..404..405..406..407..408..409..410..411..412..413..414..415..416..417..418..419..420..421..422..423..424..425..426..427..428..429..430..431..432..433..434..435..436..437..438..439..440..441..442..443..444..445..446..447..448..449..450..451..452..453..454..455..456..457..458..459..460..461..462..463..464..465..466..467..468..469..470..471..472..473..474..475..476..477..478..479..480..481..482..483..484..485..486..487..488..489..490..491..492..493..494..495..496..497..498..499..500..501..502..503..504..505..506..507..508..509..510..511..512..513..514..515..516..517..518..519..520..521..522..523..524..525..526..527..528..529..530..531..532..533..534..535..536..537..538..539..540..541..542..543..544..545..546..547..548..549..550..551..552..553..554..555..556..557..558..559..560..561..562..563..564..565..566..567..568..569..570..571..572..573..574..575..576..577..578..579..580..581..582..583..584..585..586..587..588..589..590..591..592..593..594..595..596..597..598..599..600..601..602..603..604..605..606..607..608..609..610..611..612..613..614..615..616..617..618..619..620..621..622..623..624..625..626..627..628..629..630..631..632..633..634..635..636..637..638..639..640..641..642..643..644..645..646..647..648..649..650..651..652..653..654..655..656..657..658..659..660..661..662..663..664..665..666..667..668..669..670..671..672..673..674..675..676..677..678..679..680..681..682..683..684..685..686..687..688..689..690..691..692..693..694..695..696..697..698..699..700..701..702..703..704..705..706..707..708..709..710..711..712..713..714..715..716..717..718..719..720..721..722..723..724..725..726..727..728..729..730..731..732..733..734..735..736..737..738..739..740..741..742..743..744..745..746..747..748..749..750..751..752..753..754..755..756..757..758..759..760..761..762..763..764..765..766..767..768..769..770..771..772..773..774..775..776..777..778..779..780..781..782..783..784..785..786..787..788..789..790..791..792..793..794..795..796..797..798..799..800..801..802..803..804..805..806..807..808..809..810..811..812..813..814..815..816..817..818..819..820..821..822..823..824..825..826..827..828..829..830..831..832..833..834..835..836..837..838..839..840..841..842..843..844..845..846..847..848..849..850..851..852..853..854..855..856..857..858..859..860..861..862..863..864..865..866..867..868..869..870..871..872..873..874..875..876..877..878..879..880..881..882..883..884..885..886..887..888..889..890..891..892..893..894..895..896..897..898..899..900..901..902..903..904..905..906..907..908..909..910..911..912..913..914..915..916..917..918..919..920..921..922..923..924..925..926..927..928..929..930..931..932..933..934..935..936..937..938..939..940..941..942..943..944..945..946..947..948..949..950..951..952..953..954..955..956..957..958..959..960..961..962..963..964..965..966..967..968..969..970..971..972..973..974..975..976..977..978..979..980..981..982..983..984..985..986..987..988..989..990..991..992..993..994..995..996..997..998..999..1000..1001..1002..1003..1004..1005..1006..1007..1008..1009..1010..1011..1012..1013..1014..1015..1016..1017..1018..1019..1020..1021..1022..1023..1024..1025..1026..1027..1028..1029..1030..1031..1032..1033..1034..1035..1036..1037..1038..1039..1040..1041..1042..1043..1044..1045..1046..1047..1048..1049..1050..1051..1052..1053..1054..1055..1056..1057..1058..1059..1060..1061..1062..1063..1064..1065..1066..1067..1068..1069..1070..1071..1072..1073..1074..1075..1076..1077..1078..1079..1080..1081..1082..1083..1084..1085..1086..1087..1088..1089..1090..1091..1092..1093..1094..1095..1096..1097..1098..1099..1100..1101..1102..1103..1104..1105..1106..1107..1108..1109..1110..1111..1112..1113..1114..1115..1116..1117..1118..1119..1120..1121..1122..1123..1124..1125..1126..1127..1128..1129..1130..1131..1132..1133..1134..1135..1136..1137..1138..1139..1140..1141..1142..1143..1144..1145..1146..1147..1148..1149..1150..1151..1152..1153..1154..1155..1156..1157..1158..1159..1160..1161..1162..1163..1164..1165..1166..1167..1168..1169..1170..1171..1172..1173..1174..1175..1176..1177..1178..1179..1180..1181..1182..1183..1184..1185..1186..1187..1188..1189..1190..1191..1192..1193..1194..1195..1196..1197..1198..1199..1200..1201..1202..1203..1204..1205..1206..1207..1208..1209..1210..1211.. ++ CPU time for realignment=91.4 s [=0.0754 s/sub-brick] ++ Min : roll=-0.177 pitch=-1.988 yaw=-0.385 dS=-0.963 dL=-0.136 dP=-0.670 ++ Mean: roll=-0.061 pitch=-0.245 yaw=-0.109 dS=-0.187 dL=+0.007 dP=+0.063 ++ Max : roll=+0.080 pitch=+1.809 yaw=+0.063 dS=+0.673 dL=+0.139 dP=+0.610 ++ Max displacements (mm) for each sub-brick: 1.13 1.09 1.10 1.18 1.16 1.06 1.05 1.06 1.16 1.23 1.15 1.09 1.10 1.19 1.17 1.11 1.09 1.12 1.20 1.19 1.10 1.11 1.20 1.19 1.12 1.07 1.07 1.13 1.02 0.90 0.98 1.08 0.91 0.79 0.75 0.79 0.90 0.89 0.84 0.84 0.91 0.93 0.88 0.82 0.82 0.91 0.93 0.86 0.78 0.76 0.82 0.79 0.74 0.70 0.75 0.82 0.85 0.79 0.70 0.77 0.84 0.79 0.72 0.75 0.83 0.86 0.80 0.79 0.85 0.84 0.79 0.81 0.89 0.87 0.81 0.78 0.78 0.83 0.80 0.73 0.81 0.92 0.87 0.78 0.84 0.87 0.82 0.85 0.87 0.81 0.83 0.90 0.84 0.79 0.72 0.65 0.63 0.74 0.73 0.70 0.71 0.80 0.90 0.86 0.78 0.79 0.85 0.80 0.73 0.75 0.82 0.86 0.80 0.75 0.78 0.81 0.78 0.75 0.76 0.76 0.82 0.89 0.89 0.82 0.85 0.89 0.85 0.79 0.76 0.82 0.94 0.84 0.67 0.63 0.80 0.78 0.71 0.72 0.75 0.76 0.65 0.81 1.01 1.10 1.15 1.21 1.25 1.59 1.47 1.52 1.46 1.36 1.34 1.37 1.31 1.19 1.18 1.22 1.17 1.14 1.17 1.19 1.19 1.16 1.20 1.18 1.15 1.15 1.18 1.19 1.17 1.18 1.19 1.16 1.15 1.18 1.17 1.14 1.14 1.16 1.20 1.18 1.10 1.09 1.14 1.15 1.14 1.12 1.15 1.14 1.12 1.12 1.15 1.13 1.16 1.14 1.14 1.19 1.24 1.17 1.16 1.51 2.06 1.73 1.44 1.43 1.50 1.44 1.45 1.45 1.45 1.43 1.36 1.36 1.37 1.34 1.31 1.30 1.30 1.33 1.32 1.20 1.25 1.36 1.37 1.37 1.32 1.36 1.41 1.38 1.31 1.20 1.22 1.28 1.25 1.22 1.26 1.22 1.22 1.20 1.18 1.20 1.24 1.24 1.22 1.18 1.18 1.19 1.21 1.22 1.19 1.18 1.20 1.22 1.18 1.16 1.16 1.17 1.15 1.16 1.15 1.15 1.12 1.09 1.11 1.12 1.11 1.11 1.09 1.13 1.17 1.15 1.09 1.10 1.11 1.09 1.07 1.10 1.12 1.09 1.07 1.01 0.96 0.96 1.04 1.09 1.09 1.06 1.00 0.91 0.92 0.87 0.91 1.00 1.05 1.01 0.97 0.97 0.96 0.97 0.95 0.95 0.94 0.96 0.95 0.93 0.91 0.92 0.90 0.85 0.83 0.83 0.85 0.83 0.82 0.83 0.85 0.85 0.84 0.83 0.83 0.81 0.79 0.77 0.76 0.76 0.75 0.75 0.72 0.72 0.74 0.72 0.71 0.72 0.74 0.66 0.65 0.67 0.66 0.64 0.62 0.62 0.65 0.64 0.63 0.63 0.64 0.69 0.71 0.66 0.59 0.52 0.53 0.55 0.57 0.55 0.55 0.53 0.55 0.57 0.56 0.50 0.53 0.60 0.70 0.51 0.47 0.51 0.52 0.46 0.43 0.43 0.44 0.44 0.43 0.43 0.43 0.48 0.47 0.43 0.46 0.44 0.40 0.42 0.41 0.41 0.40 0.44 0.45 0.41 0.40 0.42 0.40 0.38 0.36 0.36 0.37 0.37 0.33 0.30 0.32 0.34 0.31 0.32 0.32 0.32 0.30 0.31 0.35 0.36 0.33 0.35 0.35 0.32 0.32 0.31 0.30 0.29 0.27 0.28 0.28 0.29 0.28 0.27 0.26 0.27 0.26 0.29 0.27 0.26 0.28 0.27 0.27 0.27 0.27 0.29 0.28 0.29 0.29 0.30 0.29 0.29 0.29 0.30 0.30 0.32 0.30 0.31 0.30 0.30 0.30 0.30 0.30 0.31 0.32 0.32 0.30 0.30 0.30 0.30 0.31 0.30 0.30 0.33 0.32 0.42 0.34 0.57 0.73 0.66 0.64 0.65 0.68 0.70 0.57 0.57 0.64 0.70 0.59 0.57 0.64 0.66 0.61 0.64 0.70 0.75 0.67 0.67 0.71 0.73 0.70 0.65 0.71 0.73 0.79 0.73 0.68 0.76 0.80 0.69 0.67 0.71 0.78 0.78 0.77 2.11 1.21 1.08 0.88 0.86 0.73 0.69 0.72 0.78 0.82 0.79 0.82 0.84 0.84 0.79 0.73 0.79 0.77 0.75 1.00 1.08 1.05 0.98 0.95 0.97 0.98 0.99 0.97 1.04 1.11 1.09 1.03 1.03 1.07 1.10 1.01 0.96 0.99 1.00 0.90 0.96 1.03 1.04 0.98 0.97 1.05 1.08 1.04 1.05 1.10 1.05 1.09 1.05 0.92 1.08 1.10 0.99 1.00 1.10 1.14 1.30 1.34 1.20 1.12 1.36 1.43 1.10 1.10 1.12 1.11 0.85 0.77 0.67 0.62 0.66 0.56 0.76 0.84 0.88 0.88 0.76 0.90 0.91 0.83 0.87 0.89 0.95 0.98 0.88 0.90 0.93 0.95 0.84 0.66 0.56 1.75 1.33 0.83 0.68 0.33 0.11 0.00 0.12 0.22 0.30 0.35 0.38 0.35 0.22 0.15 0.20 0.22 0.26 0.29 0.35 0.37 0.33 0.26 0.28 0.30 0.36 0.38 0.28 0.30 0.86 3.10 2.72 1.42 0.66 0.50 0.53 0.57 0.56 0.49 0.45 0.47 0.48 0.47 0.45 0.36 0.37 0.43 0.44 0.37 0.35 0.40 0.38 0.36 0.41 0.42 0.40 0.34 0.37 0.41 0.40 0.36 0.36 0.42 0.44 0.45 0.43 0.35 0.35 0.38 0.41 0.37 0.32 0.33 0.36 0.36 0.31 0.26 0.26 0.34 0.36 0.33 0.32 0.39 0.43 0.40 0.35 0.34 0.41 0.34 0.33 0.29 0.33 0.38 0.33 0.28 0.30 0.35 0.33 0.29 0.33 0.37 0.37 0.33 0.28 0.31 0.36 0.38 0.35 0.32 0.36 0.40 0.36 0.31 0.32 0.36 0.34 0.32 0.35 0.40 0.47 0.35 0.35 0.36 0.32 0.28 0.33 0.34 0.31 0.34 0.39 0.41 0.39 0.33 0.35 0.36 0.36 0.38 0.34 0.32 0.36 0.38 0.34 0.31 0.35 0.38 0.33 0.33 0.36 0.37 0.32 0.29 0.34 0.37 0.37 0.31 0.34 0.42 0.45 0.43 0.39 0.31 0.33 0.37 0.39 0.34 0.31 0.29 0.35 0.40 0.37 0.32 0.36 0.38 0.41 0.34 0.33 0.38 0.40 0.40 0.32 0.31 0.37 0.39 0.38 0.44 0.45 0.38 0.34 0.39 0.41 0.41 0.36 0.32 0.35 0.38 0.36 0.30 0.32 0.34 0.34 0.30 0.26 0.24 0.25 0.22 0.29 0.41 0.49 0.47 0.36 0.34 0.32 0.28 0.25 0.21 0.21 0.27 0.33 0.38 0.40 0.33 0.31 0.32 0.32 0.26 0.31 0.33 0.31 0.27 0.30 0.31 0.24 0.31 0.34 0.34 0.32 0.27 0.99 1.24 1.76 3.59 3.25 3.02 2.97 2.96 2.79 2.64 2.58 2.93 3.04 2.85 2.84 2.92 2.93 2.91 2.91 2.87 2.87 2.89 2.88 2.88 2.82 2.79 2.80 2.77 2.76 2.79 2.75 2.71 2.72 2.75 2.70 2.67 2.66 2.67 2.66 2.61 2.62 2.59 2.54 2.52 2.50 2.50 2.50 2.51 2.51 2.49 2.52 2.53 2.52 2.46 2.45 2.46 2.48 2.48 2.50 2.52 2.49 2.48 2.46 2.50 2.49 2.50 2.51 2.52 2.48 2.48 2.46 2.48 2.51 2.46 2.44 2.44 2.51 2.39 2.38 2.37 2.51 2.44 2.36 2.26 2.34 2.43 2.27 2.33 2.43 2.41 2.49 2.52 2.60 2.53 2.46 2.52 2.55 2.47 2.44 2.49 2.52 2.46 2.41 2.41 2.47 2.51 2.49 2.45 2.44 2.50 2.56 2.47 2.59 2.69 2.67 2.59 2.65 2.70 2.61 2.54 2.54 2.60 2.62 2.54 2.51 2.50 2.58 2.58 2.56 2.50 2.48 2.57 2.54 2.43 2.37 2.39 2.45 2.38 2.29 2.28 2.41 2.50 2.44 2.50 2.60 2.53 2.47 2.48 2.55 2.52 2.45 2.44 2.41 2.40 2.39 2.49 2.53 2.49 2.43 2.41 2.46 2.46 2.39 2.42 2.49 2.47 2.40 2.41 2.50 2.46 2.40 2.41 2.45 2.39 2.35 2.41 2.42 2.36 2.36 2.40 2.38 2.34 2.35 2.41 2.38 2.33 2.36 2.43 2.41 2.32 2.39 2.46 2.42 2.34 2.35 2.43 2.37 2.32 2.34 2.41 2.40 2.34 2.32 2.36 2.33 1.93 1.70 1.94 2.08 2.20 2.18 2.28 2.29 2.22 2.24 2.39 2.45 2.39 2.39 2.47 2.50 2.42 2.31 2.36 2.49 2.49 2.39 2.18 2.12 2.06 2.08 2.22 2.23 2.17 2.18 2.27 2.41 2.45 2.36 2.28 2.27 2.34 2.40 2.32 2.23 2.23 2.28 2.34 2.32 2.24 2.21 2.24 2.28 2.22 2.17 2.19 2.29 2.29 2.17 2.12 2.24 2.27 2.21 2.18 2.16 2.18 2.21 2.18 2.13 2.12 2.21 2.27 2.16 2.07 2.05 2.14 2.23 2.16 2.09 2.13 2.20 2.20 2.07 2.02 2.11 2.15 2.05 1.91 1.97 2.05 1.97 1.88 1.89 1.98 1.95 1.85 1.74 1.81 1.88 1.80 1.73 1.77 1.87 1.83 1.75 1.82 1.90 1.87 1.74 1.70 1.82 1.81 1.54 1.51 1.65 1.79 1.66 1.50 1.50 1.61 1.61 1.55 1.64 1.69 1.54 1.48 1.54 1.56 1.47 1.42 1.53 1.53 1.34 1.26 1.35 1.35 1.22 1.15 1.24 1.29 1.16 1.12 1.19 1.29 1.29 1.13 1.05 1.11 1.16 1.07 1.11 1.26 1.21 1.11 1.06 1.10 1.12 1.04 1.01 1.04 1.08 0.98 0.96 0.94 1.00 1.03 0.96 0.90 0.93 0.99 0.92 0.83 0.86 0.98 0.92 ++ Max displacement in automask = 3.59 (mm) at sub-brick 840 ++ Wrote dataset to disk in 006/tmp.mc-afni2.94835/outvol.nii.gz #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 006/tmp.mc-afni2.94835/outvol.nii.gz 006/fmcpr.nii.gz --in_like 006/template.nii.gz mri_convert 006/tmp.mc-afni2.94835/outvol.nii.gz 006/fmcpr.nii.gz --in_like 006/template.nii.gz reading info from 006/template.nii.gz... INFO: This is an unsigined short. reading from 006/tmp.mc-afni2.94835/outvol.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 INFO: frames are not the same i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) writing to 006/fmcpr.nii.gz... ... cleaning up .... Tue Jun 17 14:53:19 EDT 2025 mc-afni2 done INFO: Making external regressor from mc params mcdat2mcextreg --i 006/fmcpr.mcdat --o 006/mcprextreg Tue Jun 17 14:53:19 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/fsfast/bin/mcdat2mcextreg --i 006/fmcpr.mcdat --o 006/mcprextreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmpdir.mcdat2extreg.96084/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmpdir.mcdat2extreg.96084/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmpdir.mcdat2extreg.96084/y.out.nii --pca 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmpdir.mcdat2extreg.96084/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmpdir.mcdat2extreg.96084/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmpdir.mcdat2extreg.96084/y.out.nii --pca sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmpdir.mcdat2extreg.96084/table.dat logyflag 0 usedti 0 glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmpdir.mcdat2extreg.96084/glm IllCondOK 0 ReScaleX 1 DoFFx 0 SigUseDouble 1 Creating output directory /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmpdir.mcdat2extreg.96084/glm Loading y from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmpdir.mcdat2extreg.96084/table.dat Found 6 data colums Found 1212 data rows Saving design matrix to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmpdir.mcdat2extreg.96084/glm/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 1211 Starting fit and test Fit completed in 1.66667e-05 minutes Writing results osgm maxvox sig=-284.722 F=2343.77 at index 2 0 0 seed=1750292414 Computing efficiency Measure:MC osgm Tx 171.610 Ty 41.672 Tz 284.722 Rx 60.391 Ry 4.204 Rz 21.266 Computing PCA (1212) mri_glmfit done ninputs = 1 Checking inputs nframestot = 1212 Allocing output Done allocing nframes = 1212 Computing PCA Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmpdir.mcdat2extreg.96084/pca.nii mcdat2mcextreg done ------- ************************** ----------- ------- Motion Correcting Run 007 ----------- ------- ************************** ----------- sess = 20240801_dw204 Tue Jun 17 14:53:26 EDT 2025 mc-afni2 --i 007/f.nii --t 007/template.nii.gz --o 007/fmcpr.nii.gz --mcdat 007/fmcpr.mcdat /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_info --nframes --o /tmp/mriinfo.96148 007/template.nii.gz INFO: This is an unsigined short. log file is 007/fmcpr.nii.gz.mclog mcdat file is 007/fmcpr.mcdat tmp dir is 007/tmp.mc-afni2.96148 #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 007/template.nii.gz 007/tmp.mc-afni2.96148/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 007/template.nii.gz 007/tmp.mc-afni2.96148/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 reading from 007/template.nii.gz... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) changing data type from ushrt to float (noscale = 0)... writing to 007/tmp.mc-afni2.96148/tempvol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 007/f.nii 007/tmp.mc-afni2.96148/invol.nii.gz -odt float mri_convert 007/f.nii 007/tmp.mc-afni2.96148/invol.nii.gz -odt float reading from 007/f.nii... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) changing data type from ushrt to float (noscale = 0)... writing to 007/tmp.mc-afni2.96148/invol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold 3dvolreg.afni -verbose -dfile 007/fmcpr.mcdat -1Dmatrix_save 007/fmcpr.mat -base 007/tmp.mc-afni2.96148/tempvol.nii.gz -prefix 007/tmp.mc-afni2.96148/outvol.nii.gz 007/tmp.mc-afni2.96148/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (May 22 2013) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 007/tmp.mc-afni2.96148/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:007/tmp.mc-afni2.96148/tempvol.nii.gz is 21.899994 degrees from plumb. ++ Reading in base dataset 007/tmp.mc-afni2.96148/tempvol.nii.gz ++ Oblique dataset:007/tmp.mc-afni2.96148/invol.nii.gz is 21.899994 degrees from plumb. ++ Reading input dataset 007/tmp.mc-afni2.96148/invol.nii.gz ++ Edging: x=6 y=6 z=3 ++ Creating mask for -maxdisp + Automask has 197018 voxels + 17817 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 460 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237..238..239..240..241..242..243..244..245..246..247..248..249..250..251..252..253..254..255..256..257..258..259..260..261..262..263..264..265..266..267..268..269..270..271..272..273..274..275..276..277..278..279..280..281..282..283..284..285..286..287..288..289..290..291..292..293..294..295..296..297..298..299..300..301..302..303..304..305..306..307..308..309..310..311..312..313..314..315..316..317..318..319..320..321..322..323..324..325..326..327..328..329..330..331..332..333..334..335..336..337..338..339..340..341..342..343..344..345..346..347..348..349..350..351..352..353..354..355..356..357..358..359..360..361..362..363..364..365..366..367..368..369..370..371..372..373..374..375..376..377..378..379..380..381..382..383..384..385..386..387..388..389..390..391..392..393..394..395..396..397..398..399..400..401..402..403..404..405..406..407..408..409..410..411..412..413..414..415..416..417..418..419..420..421..422..423..424..425..426..427..428..429..430..431..432..433..434..435..436..437..438..439..440..441..442..443..444..445..446..447..448..449..450..451..452..453..454..455..456..457..458..459.. ++ CPU time for realignment=29.4 s [=0.064 s/sub-brick] ++ Min : roll=-0.143 pitch=-0.481 yaw=-0.178 dS=-0.592 dL=-0.067 dP=-0.926 ++ Mean: roll=+0.058 pitch=-0.142 yaw=+0.163 dS=+0.265 dL=+0.071 dP=-0.102 ++ Max : roll=+0.409 pitch=+0.825 yaw=+0.328 dS=+1.123 dL=+0.212 dP=+0.312 ++ Max displacements (mm) for each sub-brick: 0.61 0.59 0.62 0.66 0.65 0.61 0.60 0.62 0.68 0.64 0.59 0.55 0.60 0.59 0.55 0.56 0.55 0.51 0.48 0.53 0.56 0.53 0.51 0.50 1.12 1.32 1.12 0.97 0.89 0.88 0.90 0.80 0.77 0.75 0.78 0.83 0.77 0.73 0.73 0.78 0.75 0.70 0.63 0.69 0.79 0.74 0.73 0.76 0.72 0.62 0.55 0.55 0.60 0.51 0.47 0.54 0.50 0.47 0.43 0.51 0.50 0.45 0.44 0.56 0.60 0.52 0.47 0.48 0.53 0.50 0.48 0.56 0.54 0.49 0.51 0.58 0.52 0.48 0.53 0.54 0.50 0.48 0.55 0.54 0.49 0.48 0.53 0.48 0.45 0.51 0.51 0.48 0.47 0.53 0.52 0.47 0.44 0.49 0.52 0.49 0.45 0.45 0.63 0.77 0.70 0.73 0.79 0.60 0.71 0.64 0.59 0.58 0.58 0.59 0.59 0.58 0.59 0.59 0.59 0.60 0.60 0.61 0.59 0.62 0.64 0.68 0.63 0.58 0.40 0.37 0.34 0.48 0.41 0.44 0.48 0.48 0.33 0.24 0.30 1.47 1.68 1.46 1.27 1.01 0.83 0.71 0.66 0.64 0.56 0.51 0.48 0.48 0.44 0.41 0.39 0.39 0.40 0.40 0.40 0.36 0.33 0.39 0.39 0.32 0.30 0.32 0.31 0.30 0.27 0.21 0.14 0.20 0.14 0.12 0.14 0.10 0.09 0.09 0.06 0.12 0.11 0.11 0.10 0.11 0.14 0.11 0.07 0.07 0.06 0.09 0.07 0.10 0.08 0.11 0.11 0.11 0.08 0.09 0.07 0.09 0.06 0.09 0.04 0.07 0.06 0.06 0.08 0.07 0.06 0.06 0.03 0.06 0.07 0.07 0.06 0.11 0.11 0.08 0.05 0.11 0.12 0.08 0.07 0.11 0.08 0.04 0.08 0.11 0.09 0.09 0.00 0.09 0.08 0.08 0.04 0.15 0.17 0.12 0.08 0.14 0.12 0.10 0.12 0.18 0.15 0.12 0.45 1.16 1.42 1.77 0.97 1.46 1.74 1.44 1.10 1.07 1.16 1.27 1.37 1.24 1.22 1.25 1.26 1.21 1.19 1.15 1.10 1.12 1.13 1.14 1.12 1.16 1.16 1.15 1.12 1.10 1.09 1.12 1.10 1.14 1.09 1.17 1.23 1.18 1.13 1.13 1.20 1.24 1.22 1.22 1.26 1.26 1.23 1.23 1.26 1.27 1.26 1.20 1.16 1.21 1.22 1.22 1.23 1.19 1.21 1.24 1.23 1.21 1.18 1.20 1.22 1.23 1.21 1.20 1.24 1.25 1.27 1.25 1.23 1.25 1.27 1.23 1.25 1.29 1.32 1.30 1.31 1.38 1.37 1.34 1.29 1.35 1.37 1.37 1.38 1.36 1.40 1.42 1.40 1.34 1.39 1.41 1.39 1.36 1.40 1.42 1.41 1.34 1.37 1.37 1.37 1.34 1.39 1.41 1.40 1.38 1.44 1.46 1.44 1.38 1.44 1.47 1.46 1.41 1.43 1.48 1.49 1.47 1.47 1.53 1.55 1.52 1.53 1.53 1.54 1.51 1.42 1.47 1.49 1.45 1.25 1.27 1.29 1.28 1.21 1.17 1.31 1.28 1.14 1.11 1.09 1.06 1.03 1.04 1.05 1.01 1.02 1.06 1.04 0.98 0.99 1.00 0.98 0.93 0.96 0.98 1.01 0.98 0.94 0.99 0.99 0.94 0.97 0.99 0.94 0.96 0.99 1.00 1.00 0.94 0.84 0.94 0.97 0.94 0.89 0.90 0.96 0.97 0.91 0.89 0.96 0.95 0.97 0.94 0.92 0.96 0.96 0.94 0.93 0.97 0.98 0.93 0.94 0.98 0.97 0.93 0.97 0.98 0.96 0.98 1.00 0.98 0.90 0.94 0.99 0.97 0.94 0.95 0.98 0.96 ++ Max displacement in automask = 1.77 (mm) at sub-brick 249 ++ Wrote dataset to disk in 007/tmp.mc-afni2.96148/outvol.nii.gz #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold mri_convert 007/tmp.mc-afni2.96148/outvol.nii.gz 007/fmcpr.nii.gz --in_like 007/template.nii.gz mri_convert 007/tmp.mc-afni2.96148/outvol.nii.gz 007/fmcpr.nii.gz --in_like 007/template.nii.gz reading info from 007/template.nii.gz... INFO: This is an unsigined short. reading from 007/tmp.mc-afni2.96148/outvol.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 INFO: frames are not the same i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) writing to 007/fmcpr.nii.gz... ... cleaning up .... Tue Jun 17 15:09:08 EDT 2025 mc-afni2 done INFO: Making external regressor from mc params mcdat2mcextreg --i 007/fmcpr.mcdat --o 007/mcprextreg Tue Jun 17 15:09:09 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DW204 cd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold /Applications/freesurfer/fsfast/bin/mcdat2mcextreg --i 007/fmcpr.mcdat --o 007/mcprextreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmpdir.mcdat2extreg.96379/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmpdir.mcdat2extreg.96379/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmpdir.mcdat2extreg.96379/y.out.nii --pca 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold cmdline mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmpdir.mcdat2extreg.96379/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmpdir.mcdat2extreg.96379/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmpdir.mcdat2extreg.96379/y.out.nii --pca sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmpdir.mcdat2extreg.96379/table.dat logyflag 0 usedti 0 glmdir /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmpdir.mcdat2extreg.96379/glm IllCondOK 0 ReScaleX 1 DoFFx 0 SigUseDouble 1 Creating output directory /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmpdir.mcdat2extreg.96379/glm Loading y from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmpdir.mcdat2extreg.96379/table.dat Found 6 data colums Found 460 data rows Saving design matrix to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmpdir.mcdat2extreg.96379/glm/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 459 Starting fit and test Fit completed in 1.66667e-05 minutes Writing results osgm maxvox sig=135.918 F=1311.54 at index 2 0 0 seed=1751147017 Computing efficiency Measure:MC osgm Tx 52.762 Ty 45.396 Tz 135.918 Rx 43.997 Ry 130.956 Rz 26.708 Computing PCA (460) mri_glmfit done ninputs = 1 Checking inputs nframestot = 460 Allocing output Done allocing nframes = 460 Computing PCA Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmpdir.mcdat2extreg.96379/pca.nii mcdat2mcextreg done Tue Jun 17 15:09:11 EDT 2025 mc-sess completed SUCCESSFULLY 20240801_dw204 STC ----------------------------- stc-sess -i fmcpr -o fmcpr.up -ngroups 1 -so up -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -update Tue Jun 17 15:09:11 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DW204 /Applications/freesurfer/fsfast/bin/stc-sess -i fmcpr -o fmcpr.up -ngroups 1 -so up -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -update FreeSurferEnv.csh 7.4.1 mac-mvqmt7cvdq.ddns.med.umich.edu 20240801_dw204 ----------------- Tue Jun 17 15:09:11 EDT 2025 --------------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204 stc.fsl --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.nii.gz --ngroups 1 --up Tue Jun 17 15:09:11 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DW204 /Applications/freesurfer/fsfast/bin/stc.fsl --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.nii.gz --ngroups 1 --up FreeSurferEnv.csh 7.4.1 mac-mvqmt7cvdq.ddns.med.umich.edu /Volumes/umms-hillmera/asem_ptsd/DW204 mri_info --nslices --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmp.96516/nslices.dat /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.nii.gz nslices = 176 slicedelay --nslices 176 --up --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmp.96516/sdf.txt --ngroups 1 sdf /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmp.96516/sdf.txt nslices 176 order up ngroups 1 nslicespg 176 [0.4971590909090909, 0.4914772727272727, 0.48579545454545453, 0.48011363636363635, 0.4744318181818182, 0.46875, 0.4630681818181818, 0.45738636363636365, 0.45170454545454547, 0.4460227272727273, 0.4403409090909091, 0.4346590909090909, 0.4289772727272727, 0.42329545454545453, 0.41761363636363635, 0.4119318181818182, 0.40625, 0.4005681818181818, 0.39488636363636365, 0.38920454545454547, 0.3835227272727273, 0.3778409090909091, 0.3721590909090909, 0.3664772727272727, 0.36079545454545453, 0.35511363636363635, 0.3494318181818182, 0.34375, 0.3380681818181818, 0.33238636363636365, 0.32670454545454547, 0.3210227272727273, 0.3153409090909091, 0.3096590909090909, 0.3039772727272727, 0.29829545454545453, 0.29261363636363635, 0.2869318181818182, 0.28125, 0.2755681818181818, 0.26988636363636365, 0.26420454545454547, 0.2585227272727273, 0.2528409090909091, 0.2471590909090909, 0.24147727272727273, 0.23579545454545456, 0.23011363636363635, 0.22443181818181818, 0.21875, 0.21306818181818182, 0.20738636363636365, 0.20170454545454544, 0.19602272727272727, 0.1903409090909091, 0.1846590909090909, 0.17897727272727273, 0.17329545454545456, 0.16761363636363635, 0.16193181818181818, 0.15625, 0.15056818181818182, 0.14488636363636365, 0.13920454545454544, 0.13352272727272727, 0.1278409090909091, 0.12215909090909091, 0.11647727272727272, 0.11079545454545454, 0.10511363636363637, 0.09943181818181818, 0.09375, 0.08806818181818182, 0.08238636363636363, 0.07670454545454546, 0.07102272727272728, 0.06534090909090909, 0.05965909090909091, 0.05397727272727273, 0.048295454545454544, 0.04261363636363636, 0.036931818181818184, 0.03125, 0.02556818181818182, 0.019886363636363636, 0.014204545454545454, 0.008522727272727272, 0.002840909090909091, -0.002840909090909091, -0.008522727272727272, -0.014204545454545454, -0.019886363636363636, -0.02556818181818182, -0.03125, -0.036931818181818184, -0.04261363636363636, -0.048295454545454544, -0.05397727272727273, -0.05965909090909091, -0.06534090909090909, -0.07102272727272728, -0.07670454545454546, -0.08238636363636363, -0.08806818181818182, -0.09375, -0.09943181818181818, -0.10511363636363637, -0.11079545454545454, -0.11647727272727272, -0.12215909090909091, -0.1278409090909091, -0.13352272727272727, -0.13920454545454544, -0.14488636363636365, -0.15056818181818182, -0.15625, -0.16193181818181818, -0.16761363636363635, -0.17329545454545456, -0.17897727272727273, -0.1846590909090909, -0.1903409090909091, -0.19602272727272727, -0.20170454545454544, -0.20738636363636365, -0.21306818181818182, -0.21875, -0.22443181818181818, -0.23011363636363635, -0.23579545454545456, -0.24147727272727273, -0.2471590909090909, -0.2528409090909091, -0.2585227272727273, -0.26420454545454547, -0.26988636363636365, -0.2755681818181818, -0.28125, -0.2869318181818182, -0.29261363636363635, -0.29829545454545453, -0.3039772727272727, -0.3096590909090909, -0.3153409090909091, -0.3210227272727273, -0.32670454545454547, -0.33238636363636365, -0.3380681818181818, -0.34375, -0.3494318181818182, -0.35511363636363635, -0.36079545454545453, -0.3664772727272727, -0.3721590909090909, -0.3778409090909091, -0.3835227272727273, -0.38920454545454547, -0.39488636363636365, -0.4005681818181818, -0.40625, -0.4119318181818182, -0.41761363636363635, -0.42329545454545453, -0.4289772727272727, -0.4346590909090909, -0.4403409090909091, -0.4460227272727273, -0.45170454545454547, -0.45738636363636365, -0.4630681818181818, -0.46875, -0.4744318181818182, -0.48011363636363635, -0.48579545454545453, -0.4914772727272727, -0.4971590909090909] sg 1 ---------- Slice Delay (fraction of TR) --------------- 0.4971590909091 0.4914772727273 0.4857954545455 0.4801136363636 0.4744318181818 0.4687500000000 0.4630681818182 0.4573863636364 0.4517045454545 0.4460227272727 0.4403409090909 0.4346590909091 0.4289772727273 0.4232954545455 0.4176136363636 0.4119318181818 0.4062500000000 0.4005681818182 0.3948863636364 0.3892045454545 0.3835227272727 0.3778409090909 0.3721590909091 0.3664772727273 0.3607954545455 0.3551136363636 0.3494318181818 0.3437500000000 0.3380681818182 0.3323863636364 0.3267045454545 0.3210227272727 0.3153409090909 0.3096590909091 0.3039772727273 0.2982954545455 0.2926136363636 0.2869318181818 0.2812500000000 0.2755681818182 0.2698863636364 0.2642045454545 0.2585227272727 0.2528409090909 0.2471590909091 0.2414772727273 0.2357954545455 0.2301136363636 0.2244318181818 0.2187500000000 0.2130681818182 0.2073863636364 0.2017045454545 0.1960227272727 0.1903409090909 0.1846590909091 0.1789772727273 0.1732954545455 0.1676136363636 0.1619318181818 0.1562500000000 0.1505681818182 0.1448863636364 0.1392045454545 0.1335227272727 0.1278409090909 0.1221590909091 0.1164772727273 0.1107954545455 0.1051136363636 0.0994318181818 0.0937500000000 0.0880681818182 0.0823863636364 0.0767045454545 0.0710227272727 0.0653409090909 0.0596590909091 0.0539772727273 0.0482954545455 0.0426136363636 0.0369318181818 0.0312500000000 0.0255681818182 0.0198863636364 0.0142045454545 0.0085227272727 0.0028409090909 -0.0028409090909 -0.0085227272727 -0.0142045454545 -0.0198863636364 -0.0255681818182 -0.0312500000000 -0.0369318181818 -0.0426136363636 -0.0482954545455 -0.0539772727273 -0.0596590909091 -0.0653409090909 -0.0710227272727 -0.0767045454545 -0.0823863636364 -0.0880681818182 -0.0937500000000 -0.0994318181818 -0.1051136363636 -0.1107954545455 -0.1164772727273 -0.1221590909091 -0.1278409090909 -0.1335227272727 -0.1392045454545 -0.1448863636364 -0.1505681818182 -0.1562500000000 -0.1619318181818 -0.1676136363636 -0.1732954545455 -0.1789772727273 -0.1846590909091 -0.1903409090909 -0.1960227272727 -0.2017045454545 -0.2073863636364 -0.2130681818182 -0.2187500000000 -0.2244318181818 -0.2301136363636 -0.2357954545455 -0.2414772727273 -0.2471590909091 -0.2528409090909 -0.2585227272727 -0.2642045454545 -0.2698863636364 -0.2755681818182 -0.2812500000000 -0.2869318181818 -0.2926136363636 -0.2982954545455 -0.3039772727273 -0.3096590909091 -0.3153409090909 -0.3210227272727 -0.3267045454545 -0.3323863636364 -0.3380681818182 -0.3437500000000 -0.3494318181818 -0.3551136363636 -0.3607954545455 -0.3664772727273 -0.3721590909091 -0.3778409090909 -0.3835227272727 -0.3892045454545 -0.3948863636364 -0.4005681818182 -0.4062500000000 -0.4119318181818 -0.4176136363636 -0.4232954545455 -0.4289772727273 -0.4346590909091 -0.4403409090909 -0.4460227272727 -0.4517045454545 -0.4573863636364 -0.4630681818182 -0.4687500000000 -0.4744318181818 -0.4801136363636 -0.4857954545455 -0.4914772727273 -0.4971590909091 ----------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmp.96516/in.nii mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmp.96516/in.nii reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.nii.gz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmp.96516/in.nii... /Volumes/umms-hillmera/asem_ptsd/DW204 slicetimer.fsl -i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmp.96516/in.nii -o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmp.96516/out.nii --tcustom=/Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmp.96516/sdf.txt /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmp.96516/out.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.nii.gz mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmp.96516/out.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.nii.gz reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/tmp.96516/out.nii... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, 0, 0) writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.nii.gz... stc.fsl Done --------------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204 stc.fsl --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.nii.gz --ngroups 1 --up Tue Jun 17 15:09:22 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DW204 /Applications/freesurfer/fsfast/bin/stc.fsl --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.nii.gz --ngroups 1 --up FreeSurferEnv.csh 7.4.1 mac-mvqmt7cvdq.ddns.med.umich.edu /Volumes/umms-hillmera/asem_ptsd/DW204 mri_info --nslices --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmp.96607/nslices.dat /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.nii.gz nslices = 64 slicedelay --nslices 64 --up --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmp.96607/sdf.txt --ngroups 1 sdf /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmp.96607/sdf.txt nslices 64 order up ngroups 1 nslicespg 64 [0.4921875, 0.4765625, 0.4609375, 0.4453125, 0.4296875, 0.4140625, 0.3984375, 0.3828125, 0.3671875, 0.3515625, 0.3359375, 0.3203125, 0.3046875, 0.2890625, 0.2734375, 0.2578125, 0.2421875, 0.2265625, 0.2109375, 0.1953125, 0.1796875, 0.1640625, 0.1484375, 0.1328125, 0.1171875, 0.1015625, 0.0859375, 0.0703125, 0.0546875, 0.0390625, 0.0234375, 0.0078125, -0.0078125, -0.0234375, -0.0390625, -0.0546875, -0.0703125, -0.0859375, -0.1015625, -0.1171875, -0.1328125, -0.1484375, -0.1640625, -0.1796875, -0.1953125, -0.2109375, -0.2265625, -0.2421875, -0.2578125, -0.2734375, -0.2890625, -0.3046875, -0.3203125, -0.3359375, -0.3515625, -0.3671875, -0.3828125, -0.3984375, -0.4140625, -0.4296875, -0.4453125, -0.4609375, -0.4765625, -0.4921875] sg 1 ---------- Slice Delay (fraction of TR) --------------- 0.4921875000000 0.4765625000000 0.4609375000000 0.4453125000000 0.4296875000000 0.4140625000000 0.3984375000000 0.3828125000000 0.3671875000000 0.3515625000000 0.3359375000000 0.3203125000000 0.3046875000000 0.2890625000000 0.2734375000000 0.2578125000000 0.2421875000000 0.2265625000000 0.2109375000000 0.1953125000000 0.1796875000000 0.1640625000000 0.1484375000000 0.1328125000000 0.1171875000000 0.1015625000000 0.0859375000000 0.0703125000000 0.0546875000000 0.0390625000000 0.0234375000000 0.0078125000000 -0.0078125000000 -0.0234375000000 -0.0390625000000 -0.0546875000000 -0.0703125000000 -0.0859375000000 -0.1015625000000 -0.1171875000000 -0.1328125000000 -0.1484375000000 -0.1640625000000 -0.1796875000000 -0.1953125000000 -0.2109375000000 -0.2265625000000 -0.2421875000000 -0.2578125000000 -0.2734375000000 -0.2890625000000 -0.3046875000000 -0.3203125000000 -0.3359375000000 -0.3515625000000 -0.3671875000000 -0.3828125000000 -0.3984375000000 -0.4140625000000 -0.4296875000000 -0.4453125000000 -0.4609375000000 -0.4765625000000 -0.4921875000000 ----------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmp.96607/in.nii mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmp.96607/in.nii reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.nii.gz... TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmp.96607/in.nii... /Volumes/umms-hillmera/asem_ptsd/DW204 slicetimer.fsl -i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmp.96607/in.nii -o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmp.96607/out.nii --tcustom=/Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmp.96607/sdf.txt /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmp.96607/out.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.nii.gz mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmp.96607/out.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.nii.gz reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/tmp.96607/out.nii... TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -0.927836, -0.372988) k_ras = (0, -0.372988, 0.927836) writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.nii.gz... stc.fsl Done --------------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204 stc.fsl --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.nii.gz --ngroups 1 --up Tue Jun 17 15:09:52 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DW204 /Applications/freesurfer/fsfast/bin/stc.fsl --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.nii.gz --ngroups 1 --up FreeSurferEnv.csh 7.4.1 mac-mvqmt7cvdq.ddns.med.umich.edu /Volumes/umms-hillmera/asem_ptsd/DW204 mri_info --nslices --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmp.96704/nslices.dat /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.nii.gz nslices = 64 slicedelay --nslices 64 --up --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmp.96704/sdf.txt --ngroups 1 sdf /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmp.96704/sdf.txt nslices 64 order up ngroups 1 nslicespg 64 [0.4921875, 0.4765625, 0.4609375, 0.4453125, 0.4296875, 0.4140625, 0.3984375, 0.3828125, 0.3671875, 0.3515625, 0.3359375, 0.3203125, 0.3046875, 0.2890625, 0.2734375, 0.2578125, 0.2421875, 0.2265625, 0.2109375, 0.1953125, 0.1796875, 0.1640625, 0.1484375, 0.1328125, 0.1171875, 0.1015625, 0.0859375, 0.0703125, 0.0546875, 0.0390625, 0.0234375, 0.0078125, -0.0078125, -0.0234375, -0.0390625, -0.0546875, -0.0703125, -0.0859375, -0.1015625, -0.1171875, -0.1328125, -0.1484375, -0.1640625, -0.1796875, -0.1953125, -0.2109375, -0.2265625, -0.2421875, -0.2578125, -0.2734375, -0.2890625, -0.3046875, -0.3203125, -0.3359375, -0.3515625, -0.3671875, -0.3828125, -0.3984375, -0.4140625, -0.4296875, -0.4453125, -0.4609375, -0.4765625, -0.4921875] sg 1 ---------- Slice Delay (fraction of TR) --------------- 0.4921875000000 0.4765625000000 0.4609375000000 0.4453125000000 0.4296875000000 0.4140625000000 0.3984375000000 0.3828125000000 0.3671875000000 0.3515625000000 0.3359375000000 0.3203125000000 0.3046875000000 0.2890625000000 0.2734375000000 0.2578125000000 0.2421875000000 0.2265625000000 0.2109375000000 0.1953125000000 0.1796875000000 0.1640625000000 0.1484375000000 0.1328125000000 0.1171875000000 0.1015625000000 0.0859375000000 0.0703125000000 0.0546875000000 0.0390625000000 0.0234375000000 0.0078125000000 -0.0078125000000 -0.0234375000000 -0.0390625000000 -0.0546875000000 -0.0703125000000 -0.0859375000000 -0.1015625000000 -0.1171875000000 -0.1328125000000 -0.1484375000000 -0.1640625000000 -0.1796875000000 -0.1953125000000 -0.2109375000000 -0.2265625000000 -0.2421875000000 -0.2578125000000 -0.2734375000000 -0.2890625000000 -0.3046875000000 -0.3203125000000 -0.3359375000000 -0.3515625000000 -0.3671875000000 -0.3828125000000 -0.3984375000000 -0.4140625000000 -0.4296875000000 -0.4453125000000 -0.4609375000000 -0.4765625000000 -0.4921875000000 ----------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmp.96704/in.nii mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmp.96704/in.nii reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.nii.gz... TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmp.96704/in.nii... /Volumes/umms-hillmera/asem_ptsd/DW204 slicetimer.fsl -i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmp.96704/in.nii -o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmp.96704/out.nii --tcustom=/Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmp.96704/sdf.txt /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmp.96704/out.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.nii.gz mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmp.96704/out.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.nii.gz reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/tmp.96704/out.nii... TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -0.927836, -0.372988) k_ras = (0, -0.372988, 0.927836) writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.nii.gz... stc.fsl Done --------------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204 stc.fsl --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.nii.gz --ngroups 1 --up Tue Jun 17 15:10:22 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DW204 /Applications/freesurfer/fsfast/bin/stc.fsl --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.nii.gz --ngroups 1 --up FreeSurferEnv.csh 7.4.1 mac-mvqmt7cvdq.ddns.med.umich.edu /Volumes/umms-hillmera/asem_ptsd/DW204 mri_info --nslices --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmp.96811/nslices.dat /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.nii.gz nslices = 60 slicedelay --nslices 60 --up --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmp.96811/sdf.txt --ngroups 1 sdf /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmp.96811/sdf.txt nslices 60 order up ngroups 1 nslicespg 60 [0.49166666666666664, 0.475, 0.4583333333333333, 0.44166666666666665, 0.425, 0.4083333333333333, 0.39166666666666666, 0.375, 0.35833333333333334, 0.3416666666666667, 0.325, 0.30833333333333335, 0.2916666666666667, 0.275, 0.25833333333333336, 0.24166666666666667, 0.225, 0.20833333333333334, 0.19166666666666668, 0.175, 0.15833333333333333, 0.14166666666666666, 0.125, 0.10833333333333334, 0.09166666666666666, 0.075, 0.058333333333333334, 0.041666666666666664, 0.025, 0.008333333333333333, -0.008333333333333333, -0.025, -0.041666666666666664, -0.058333333333333334, -0.075, -0.09166666666666666, -0.10833333333333334, -0.125, -0.14166666666666666, -0.15833333333333333, -0.175, -0.19166666666666668, -0.20833333333333334, -0.225, -0.24166666666666667, -0.25833333333333336, -0.275, -0.2916666666666667, -0.30833333333333335, -0.325, -0.3416666666666667, -0.35833333333333334, -0.375, -0.39166666666666666, -0.4083333333333333, -0.425, -0.44166666666666665, -0.4583333333333333, -0.475, -0.49166666666666664] sg 1 ---------- Slice Delay (fraction of TR) --------------- 0.4916666666667 0.4750000000000 0.4583333333333 0.4416666666667 0.4250000000000 0.4083333333333 0.3916666666667 0.3750000000000 0.3583333333333 0.3416666666667 0.3250000000000 0.3083333333333 0.2916666666667 0.2750000000000 0.2583333333333 0.2416666666667 0.2250000000000 0.2083333333333 0.1916666666667 0.1750000000000 0.1583333333333 0.1416666666667 0.1250000000000 0.1083333333333 0.0916666666667 0.0750000000000 0.0583333333333 0.0416666666667 0.0250000000000 0.0083333333333 -0.0083333333333 -0.0250000000000 -0.0416666666667 -0.0583333333333 -0.0750000000000 -0.0916666666667 -0.1083333333333 -0.1250000000000 -0.1416666666667 -0.1583333333333 -0.1750000000000 -0.1916666666667 -0.2083333333333 -0.2250000000000 -0.2416666666667 -0.2583333333333 -0.2750000000000 -0.2916666666667 -0.3083333333333 -0.3250000000000 -0.3416666666667 -0.3583333333333 -0.3750000000000 -0.3916666666667 -0.4083333333333 -0.4250000000000 -0.4416666666667 -0.4583333333333 -0.4750000000000 -0.4916666666667 ----------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmp.96811/in.nii mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmp.96811/in.nii reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmp.96811/in.nii... /Volumes/umms-hillmera/asem_ptsd/DW204 slicetimer.fsl -i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmp.96811/in.nii -o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmp.96811/out.nii --tcustom=/Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmp.96811/sdf.txt /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmp.96811/out.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.nii.gz mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmp.96811/out.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.nii.gz reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/tmp.96811/out.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -0.927836, -0.372988) k_ras = (0, -0.372988, 0.927836) writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.nii.gz... stc.fsl Done --------------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204 stc.fsl --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.nii.gz --ngroups 1 --up Tue Jun 17 15:12:11 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DW204 /Applications/freesurfer/fsfast/bin/stc.fsl --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.nii.gz --ngroups 1 --up FreeSurferEnv.csh 7.4.1 mac-mvqmt7cvdq.ddns.med.umich.edu /Volumes/umms-hillmera/asem_ptsd/DW204 mri_info --nslices --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmp.96902/nslices.dat /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.nii.gz nslices = 60 slicedelay --nslices 60 --up --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmp.96902/sdf.txt --ngroups 1 sdf /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmp.96902/sdf.txt nslices 60 order up ngroups 1 nslicespg 60 [0.49166666666666664, 0.475, 0.4583333333333333, 0.44166666666666665, 0.425, 0.4083333333333333, 0.39166666666666666, 0.375, 0.35833333333333334, 0.3416666666666667, 0.325, 0.30833333333333335, 0.2916666666666667, 0.275, 0.25833333333333336, 0.24166666666666667, 0.225, 0.20833333333333334, 0.19166666666666668, 0.175, 0.15833333333333333, 0.14166666666666666, 0.125, 0.10833333333333334, 0.09166666666666666, 0.075, 0.058333333333333334, 0.041666666666666664, 0.025, 0.008333333333333333, -0.008333333333333333, -0.025, -0.041666666666666664, -0.058333333333333334, -0.075, -0.09166666666666666, -0.10833333333333334, -0.125, -0.14166666666666666, -0.15833333333333333, -0.175, -0.19166666666666668, -0.20833333333333334, -0.225, -0.24166666666666667, -0.25833333333333336, -0.275, -0.2916666666666667, -0.30833333333333335, -0.325, -0.3416666666666667, -0.35833333333333334, -0.375, -0.39166666666666666, -0.4083333333333333, -0.425, -0.44166666666666665, -0.4583333333333333, -0.475, -0.49166666666666664] sg 1 ---------- Slice Delay (fraction of TR) --------------- 0.4916666666667 0.4750000000000 0.4583333333333 0.4416666666667 0.4250000000000 0.4083333333333 0.3916666666667 0.3750000000000 0.3583333333333 0.3416666666667 0.3250000000000 0.3083333333333 0.2916666666667 0.2750000000000 0.2583333333333 0.2416666666667 0.2250000000000 0.2083333333333 0.1916666666667 0.1750000000000 0.1583333333333 0.1416666666667 0.1250000000000 0.1083333333333 0.0916666666667 0.0750000000000 0.0583333333333 0.0416666666667 0.0250000000000 0.0083333333333 -0.0083333333333 -0.0250000000000 -0.0416666666667 -0.0583333333333 -0.0750000000000 -0.0916666666667 -0.1083333333333 -0.1250000000000 -0.1416666666667 -0.1583333333333 -0.1750000000000 -0.1916666666667 -0.2083333333333 -0.2250000000000 -0.2416666666667 -0.2583333333333 -0.2750000000000 -0.2916666666667 -0.3083333333333 -0.3250000000000 -0.3416666666667 -0.3583333333333 -0.3750000000000 -0.3916666666667 -0.4083333333333 -0.4250000000000 -0.4416666666667 -0.4583333333333 -0.4750000000000 -0.4916666666667 ----------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmp.96902/in.nii mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmp.96902/in.nii reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmp.96902/in.nii... /Volumes/umms-hillmera/asem_ptsd/DW204 slicetimer.fsl -i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmp.96902/in.nii -o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmp.96902/out.nii --tcustom=/Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmp.96902/sdf.txt /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmp.96902/out.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.nii.gz mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmp.96902/out.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.nii.gz reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/tmp.96902/out.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -0.927836, -0.372988) k_ras = (0, -0.372988, 0.927836) writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.nii.gz... stc.fsl Done --------------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204 stc.fsl --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.nii.gz --ngroups 1 --up Tue Jun 17 15:48:52 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DW204 /Applications/freesurfer/fsfast/bin/stc.fsl --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.nii.gz --ngroups 1 --up FreeSurferEnv.csh 7.4.1 mac-mvqmt7cvdq.ddns.med.umich.edu /Volumes/umms-hillmera/asem_ptsd/DW204 mri_info --nslices --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmp.97273/nslices.dat /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.nii.gz nslices = 60 slicedelay --nslices 60 --up --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmp.97273/sdf.txt --ngroups 1 sdf /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmp.97273/sdf.txt nslices 60 order up ngroups 1 nslicespg 60 [0.49166666666666664, 0.475, 0.4583333333333333, 0.44166666666666665, 0.425, 0.4083333333333333, 0.39166666666666666, 0.375, 0.35833333333333334, 0.3416666666666667, 0.325, 0.30833333333333335, 0.2916666666666667, 0.275, 0.25833333333333336, 0.24166666666666667, 0.225, 0.20833333333333334, 0.19166666666666668, 0.175, 0.15833333333333333, 0.14166666666666666, 0.125, 0.10833333333333334, 0.09166666666666666, 0.075, 0.058333333333333334, 0.041666666666666664, 0.025, 0.008333333333333333, -0.008333333333333333, -0.025, -0.041666666666666664, -0.058333333333333334, -0.075, -0.09166666666666666, -0.10833333333333334, -0.125, -0.14166666666666666, -0.15833333333333333, -0.175, -0.19166666666666668, -0.20833333333333334, -0.225, -0.24166666666666667, -0.25833333333333336, -0.275, -0.2916666666666667, -0.30833333333333335, -0.325, -0.3416666666666667, -0.35833333333333334, -0.375, -0.39166666666666666, -0.4083333333333333, -0.425, -0.44166666666666665, -0.4583333333333333, -0.475, -0.49166666666666664] sg 1 ---------- Slice Delay (fraction of TR) --------------- 0.4916666666667 0.4750000000000 0.4583333333333 0.4416666666667 0.4250000000000 0.4083333333333 0.3916666666667 0.3750000000000 0.3583333333333 0.3416666666667 0.3250000000000 0.3083333333333 0.2916666666667 0.2750000000000 0.2583333333333 0.2416666666667 0.2250000000000 0.2083333333333 0.1916666666667 0.1750000000000 0.1583333333333 0.1416666666667 0.1250000000000 0.1083333333333 0.0916666666667 0.0750000000000 0.0583333333333 0.0416666666667 0.0250000000000 0.0083333333333 -0.0083333333333 -0.0250000000000 -0.0416666666667 -0.0583333333333 -0.0750000000000 -0.0916666666667 -0.1083333333333 -0.1250000000000 -0.1416666666667 -0.1583333333333 -0.1750000000000 -0.1916666666667 -0.2083333333333 -0.2250000000000 -0.2416666666667 -0.2583333333333 -0.2750000000000 -0.2916666666667 -0.3083333333333 -0.3250000000000 -0.3416666666667 -0.3583333333333 -0.3750000000000 -0.3916666666667 -0.4083333333333 -0.4250000000000 -0.4416666666667 -0.4583333333333 -0.4750000000000 -0.4916666666667 ----------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmp.97273/in.nii mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmp.97273/in.nii reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.927836, -0.372988) k_ras = (-0, -0.372988, 0.927836) writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmp.97273/in.nii... /Volumes/umms-hillmera/asem_ptsd/DW204 slicetimer.fsl -i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmp.97273/in.nii -o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmp.97273/out.nii --tcustom=/Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmp.97273/sdf.txt /Volumes/umms-hillmera/asem_ptsd/DW204 mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmp.97273/out.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.nii.gz mri_convert /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmp.97273/out.nii /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.nii.gz reading from /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/tmp.97273/out.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -0.927836, -0.372988) k_ras = (0, -0.372988, 0.927836) writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.nii.gz... stc.fsl Done Started at Tue Jun 17 15:09:11 EDT 2025 Ended at Tue Jun 17 16:00:03 EDT 2025 stc-sess Done 20240801_dw204 To Surface ----------------------------- rawfunc2surf-sess -fwhm 5 -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -trgsubject fsaverage -stc up -update -per-run instem fmcpr.up outstem fmcpr.up.sm5.fsaverage.hemi ------------------------------ 1/1 20240801_dw204 1/1 20240801_dw204 002 lh --------- Tue Jun 17 16:00:04 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.lh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- -0.03510 0.99892 -0.03050 0.64655; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01602; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 87902 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (134246) Reverse Loop had 15404 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 97074, nSrcLost = 0, nSrcMulti = 37172, MnSrcMultiHits = 2.21059 nTrg121 = 149670, nTrgMulti = 14172, MnTrgMultiHits = 2.08693 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.lh.pr.nii.gz Dim: 163842 1 1 mri_vol2surf done mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.lh.pr.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204 cmdline mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.lh.pr.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.lh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.lh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149955 values in range Counting number of voxels in first frame Found 149954 voxels in final mask Writing output to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.lh.pr.nii.gz Count: 149954 149954.000000 163842 91.523541 mri_binarize done 1/1 20240801_dw204 003 lh --------- Tue Jun 17 16:00:10 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.lh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 0.99995 -0.00300 0.00925 -0.46384; -0.00971 -0.35421 0.93512 -14.17781; -0.00047 0.93516 0.35422 10.90227; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31223 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (134246) Reverse Loop had 15404 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 97074, nSrcLost = 0, nSrcMulti = 37172, MnSrcMultiHits = 2.21059 nTrg121 = 149670, nTrgMulti = 14172, MnTrgMultiHits = 2.08693 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.lh.pr.nii.gz Dim: 163842 1 1 mri_vol2surf done mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.lh.pr.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204 cmdline mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.lh.pr.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.lh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.lh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149955 values in range Counting number of voxels in first frame Found 149954 voxels in final mask Writing output to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.lh.pr.nii.gz Count: 149954 149954.000000 163842 91.523541 mri_binarize done 1/1 20240801_dw204 004 lh --------- Tue Jun 17 16:00:12 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.lh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 0.99988 0.00031 0.01560 -0.73119; -0.01437 -0.37068 0.92865 -13.70915; -0.00607 0.92876 0.37063 12.62407; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31298 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (134246) Reverse Loop had 15404 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 97074, nSrcLost = 0, nSrcMulti = 37172, MnSrcMultiHits = 2.21059 nTrg121 = 149670, nTrgMulti = 14172, MnTrgMultiHits = 2.08693 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.lh.pr.nii.gz Dim: 163842 1 1 mri_vol2surf done mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.lh.pr.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204 cmdline mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.lh.pr.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.lh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.lh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149955 values in range Counting number of voxels in first frame Found 149954 voxels in final mask Writing output to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.lh.pr.nii.gz Count: 149954 149954.000000 163842 91.523541 mri_binarize done 1/1 20240801_dw204 005 lh --------- Tue Jun 17 16:00:14 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.lh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 0.99994 0.00665 0.00842 -0.60532; -0.00548 -0.35819 0.93363 -16.52873; -0.00923 0.93363 0.35813 12.42865; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31241 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (134246) Reverse Loop had 15404 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 97074, nSrcLost = 0, nSrcMulti = 37172, MnSrcMultiHits = 2.21059 nTrg121 = 149670, nTrgMulti = 14172, MnTrgMultiHits = 2.08693 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.lh.pr.nii.gz Dim: 163842 1 1 mri_vol2surf done mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.lh.pr.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204 cmdline mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.lh.pr.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.lh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.lh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149938 values in range Counting number of voxels in first frame Found 149937 voxels in final mask Writing output to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.lh.pr.nii.gz Count: 149937 149937.000000 163842 91.513165 mri_binarize done 1/1 20240801_dw204 006 lh --------- Tue Jun 17 16:00:16 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.lh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 0.99990 0.00705 0.01226 -0.54247; -0.00863 -0.38302 0.92370 -16.86919; -0.01121 0.92372 0.38292 12.15180; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31166 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (134246) Reverse Loop had 15404 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 97074, nSrcLost = 0, nSrcMulti = 37172, MnSrcMultiHits = 2.21059 nTrg121 = 149670, nTrgMulti = 14172, MnTrgMultiHits = 2.08693 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.lh.pr.nii.gz Dim: 163842 1 1 mri_vol2surf done mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.lh.pr.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204 cmdline mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.lh.pr.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.lh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.lh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149935 values in range Counting number of voxels in first frame Found 149934 voxels in final mask Writing output to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.lh.pr.nii.gz Count: 149934 149934.000000 163842 91.511334 mri_binarize done 1/1 20240801_dw204 007 lh --------- Tue Jun 17 16:00:19 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.lh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 0.99999 0.00199 0.00301 -0.75541; -0.00208 -0.36274 0.93189 -16.20432; -0.00295 0.93189 0.36274 12.02584; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31189 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (134246) Reverse Loop had 15404 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 97074, nSrcLost = 0, nSrcMulti = 37172, MnSrcMultiHits = 2.21059 nTrg121 = 149670, nTrgMulti = 14172, MnTrgMultiHits = 2.08693 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.lh.pr.nii.gz Dim: 163842 1 1 mri_vol2surf done mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.lh.pr.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204 cmdline mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.lh.pr.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.lh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.lh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149942 values in range Counting number of voxels in first frame Found 149941 voxels in final mask Writing output to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.lh.pr.nii.gz Count: 149941 149941.000000 163842 91.515606 mri_binarize done mri_concat --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.lh.pr.nii.gz --mean /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.lh.pr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.lh.pr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.lh.pr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.lh.pr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.lh.pr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.lh.pr.nii.gz ninputs = 6 Checking inputs nframestot = 6 Allocing output Done allocing nframes = 6 Computing mean across frames Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.lh.pr.nii.gz mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.lh.pr.nii.gz --min 10e-10 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.lh.pr.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204 cmdline mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.lh.pr.nii.gz --min 10e-10 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.lh.pr.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.lh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.lh.pr.nii.gz Binarizing based on threshold min 1e-09 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149955 values in range Counting number of voxels in first frame Found 149954 voxels in final mask Writing output to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.lh.pr.nii.gz Count: 149954 149954.000000 163842 91.523541 mri_binarize done 1/1 20240801_dw204 002 rh --------- Tue Jun 17 16:00:22 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi rh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.rh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- -0.03510 0.99892 -0.03050 0.64655; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01602; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 89107 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (136090) Reverse Loop had 17088 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 99202, nSrcLost = 0, nSrcMulti = 36888, MnSrcMultiHits = 2.21557 nTrg121 = 148228, nTrgMulti = 15614, MnTrgMultiHits = 2.0944 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.rh.pr.nii.gz Dim: 163842 1 1 mri_vol2surf done mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.rh.pr.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204 cmdline mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.rh.pr.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.rh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.rh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149926 values in range Counting number of voxels in first frame Found 149925 voxels in final mask Writing output to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.rh.pr.nii.gz Count: 149925 149925.000000 163842 91.505841 mri_binarize done 1/1 20240801_dw204 003 rh --------- Tue Jun 17 16:00:24 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi rh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.rh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 0.99995 -0.00300 0.00925 -0.46384; -0.00971 -0.35421 0.93512 -14.17781; -0.00047 0.93516 0.35422 10.90227; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31374 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (136090) Reverse Loop had 17088 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 99202, nSrcLost = 0, nSrcMulti = 36888, MnSrcMultiHits = 2.21557 nTrg121 = 148228, nTrgMulti = 15614, MnTrgMultiHits = 2.0944 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.rh.pr.nii.gz Dim: 163842 1 1 mri_vol2surf done mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.rh.pr.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204 cmdline mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.rh.pr.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.rh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.rh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149926 values in range Counting number of voxels in first frame Found 149925 voxels in final mask Writing output to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.rh.pr.nii.gz Count: 149925 149925.000000 163842 91.505841 mri_binarize done 1/1 20240801_dw204 004 rh --------- Tue Jun 17 16:00:27 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi rh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.rh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 0.99988 0.00031 0.01560 -0.73119; -0.01437 -0.37068 0.92865 -13.70915; -0.00607 0.92876 0.37063 12.62407; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31450 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (136090) Reverse Loop had 17088 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 99202, nSrcLost = 0, nSrcMulti = 36888, MnSrcMultiHits = 2.21557 nTrg121 = 148228, nTrgMulti = 15614, MnTrgMultiHits = 2.0944 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.rh.pr.nii.gz Dim: 163842 1 1 mri_vol2surf done mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.rh.pr.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204 cmdline mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.rh.pr.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.rh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.rh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149926 values in range Counting number of voxels in first frame Found 149925 voxels in final mask Writing output to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.rh.pr.nii.gz Count: 149925 149925.000000 163842 91.505841 mri_binarize done 1/1 20240801_dw204 005 rh --------- Tue Jun 17 16:00:29 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi rh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.rh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 0.99994 0.00665 0.00842 -0.60532; -0.00548 -0.35819 0.93363 -16.52873; -0.00923 0.93363 0.35813 12.42865; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31487 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (136090) Reverse Loop had 17088 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 99202, nSrcLost = 0, nSrcMulti = 36888, MnSrcMultiHits = 2.21557 nTrg121 = 148228, nTrgMulti = 15614, MnTrgMultiHits = 2.0944 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.rh.pr.nii.gz Dim: 163842 1 1 mri_vol2surf done mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.rh.pr.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204 cmdline mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.rh.pr.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.rh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.rh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149823 values in range Counting number of voxels in first frame Found 149822 voxels in final mask Writing output to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.rh.pr.nii.gz Count: 149822 149822.000000 163842 91.442976 mri_binarize done 1/1 20240801_dw204 006 rh --------- Tue Jun 17 16:00:31 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi rh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.rh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 0.99990 0.00705 0.01226 -0.54247; -0.00863 -0.38302 0.92370 -16.86919; -0.01121 0.92372 0.38292 12.15180; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31292 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (136090) Reverse Loop had 17088 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 99202, nSrcLost = 0, nSrcMulti = 36888, MnSrcMultiHits = 2.21557 nTrg121 = 148228, nTrgMulti = 15614, MnTrgMultiHits = 2.0944 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.rh.pr.nii.gz Dim: 163842 1 1 mri_vol2surf done mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.rh.pr.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204 cmdline mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.rh.pr.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.rh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.rh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149767 values in range Counting number of voxels in first frame Found 149766 voxels in final mask Writing output to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.rh.pr.nii.gz Count: 149766 149766.000000 163842 91.408796 mri_binarize done 1/1 20240801_dw204 007 rh --------- Tue Jun 17 16:00:34 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi rh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.rh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 0.99999 0.00199 0.00301 -0.75541; -0.00208 -0.36274 0.93189 -16.20432; -0.00295 0.93189 0.36274 12.02584; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31445 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (136090) Reverse Loop had 17088 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 99202, nSrcLost = 0, nSrcMulti = 36888, MnSrcMultiHits = 2.21557 nTrg121 = 148228, nTrgMulti = 15614, MnTrgMultiHits = 2.0944 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.rh.pr.nii.gz Dim: 163842 1 1 mri_vol2surf done mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.rh.pr.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204 cmdline mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.rh.pr.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.rh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.rh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149843 values in range Counting number of voxels in first frame Found 149842 voxels in final mask Writing output to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.rh.pr.nii.gz Count: 149842 149842.000000 163842 91.455182 mri_binarize done mri_concat --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.rh.pr.nii.gz --mean /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.rh.pr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.rh.pr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.rh.pr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.rh.pr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.rh.pr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.rh.pr.nii.gz ninputs = 6 Checking inputs nframestot = 6 Allocing output Done allocing nframes = 6 Computing mean across frames Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.rh.pr.nii.gz mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.rh.pr.nii.gz --min 10e-10 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.rh.pr.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204 cmdline mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.rh.pr.nii.gz --min 10e-10 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.rh.pr.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.rh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.rh.pr.nii.gz Binarizing based on threshold min 1e-09 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149926 values in range Counting number of voxels in first frame Found 149925 voxels in final mask Writing output to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.fsaverage.rh.pr.nii.gz Count: 149925 149925.000000 163842 91.505841 mri_binarize done 1/1 20240801_dw204 002 lh --------- Tue Jun 17 16:00:36 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi lh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.sm5.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA -------- original matrix ----------- -0.03510 0.99892 -0.03050 0.64655; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01602; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 87902 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (134246) Reverse Loop had 15404 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 97074, nSrcLost = 0, nSrcMulti = 37172, MnSrcMultiHits = 2.21059 nTrg121 = 149670, nTrgMulti = 14172, MnTrgMultiHits = 2.08693 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.sm5.fsaverage.lh.nii.gz Dim: 163842 1 1 mri_vol2surf done mris_fwhm --s fsaverage --hemi lh --smooth-only --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.sm5.fsaverage.lh.nii.gz --fwhm 5 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.sm5.fsaverage.lh.nii.gz --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.lh.nii.gz --no-detrend fsaverage lh white Number of vertices 163842 Number of faces 327680 Total area 65417.000000 GroupSurface 82219.960938 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.lh.nii.gz Found 149955 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=18 Only smoothing, so saving and exiting now 1/1 20240801_dw204 003 lh --------- Tue Jun 17 16:00:40 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi lh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.sm5.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA -------- original matrix ----------- 0.99995 -0.00300 0.00925 -0.46384; -0.00971 -0.35421 0.93512 -14.17781; -0.00047 0.93516 0.35422 10.90227; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31223 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (134246) Reverse Loop had 15404 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 97074, nSrcLost = 0, nSrcMulti = 37172, MnSrcMultiHits = 2.21059 nTrg121 = 149670, nTrgMulti = 14172, MnTrgMultiHits = 2.08693 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.sm5.fsaverage.lh.nii.gz Dim: 163842 1 1 mri_vol2surf done mris_fwhm --s fsaverage --hemi lh --smooth-only --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.sm5.fsaverage.lh.nii.gz --fwhm 5 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.sm5.fsaverage.lh.nii.gz --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.lh.nii.gz --no-detrend fsaverage lh white Number of vertices 163842 Number of faces 327680 Total area 65417.000000 GroupSurface 82219.960938 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.lh.nii.gz Found 149955 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=18 Only smoothing, so saving and exiting now 1/1 20240801_dw204 004 lh --------- Tue Jun 17 16:00:51 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi lh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.sm5.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA -------- original matrix ----------- 0.99988 0.00031 0.01560 -0.73119; -0.01437 -0.37068 0.92865 -13.70915; -0.00607 0.92876 0.37063 12.62407; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31298 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (134246) Reverse Loop had 15404 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 97074, nSrcLost = 0, nSrcMulti = 37172, MnSrcMultiHits = 2.21059 nTrg121 = 149670, nTrgMulti = 14172, MnTrgMultiHits = 2.08693 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.sm5.fsaverage.lh.nii.gz Dim: 163842 1 1 mri_vol2surf done mris_fwhm --s fsaverage --hemi lh --smooth-only --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.sm5.fsaverage.lh.nii.gz --fwhm 5 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.sm5.fsaverage.lh.nii.gz --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.lh.nii.gz --no-detrend fsaverage lh white Number of vertices 163842 Number of faces 327680 Total area 65417.000000 GroupSurface 82219.960938 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.lh.nii.gz Found 149955 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=18 Only smoothing, so saving and exiting now 1/1 20240801_dw204 005 lh --------- Tue Jun 17 16:01:02 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi lh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.sm5.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA -------- original matrix ----------- 0.99994 0.00665 0.00842 -0.60532; -0.00548 -0.35819 0.93363 -16.52873; -0.00923 0.93363 0.35813 12.42865; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31241 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (134246) Reverse Loop had 15404 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 97074, nSrcLost = 0, nSrcMulti = 37172, MnSrcMultiHits = 2.21059 nTrg121 = 149670, nTrgMulti = 14172, MnTrgMultiHits = 2.08693 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.sm5.fsaverage.lh.nii.gz Dim: 163842 1 1 mri_vol2surf done mris_fwhm --s fsaverage --hemi lh --smooth-only --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.sm5.fsaverage.lh.nii.gz --fwhm 5 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.sm5.fsaverage.lh.nii.gz --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.lh.nii.gz --no-detrend fsaverage lh white Number of vertices 163842 Number of faces 327680 Total area 65417.000000 GroupSurface 82219.960938 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.lh.nii.gz Found 149955 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=18 Only smoothing, so saving and exiting now 1/1 20240801_dw204 006 lh --------- Tue Jun 17 16:01:17 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi lh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.sm5.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA -------- original matrix ----------- 0.99990 0.00705 0.01226 -0.54247; -0.00863 -0.38302 0.92370 -16.86919; -0.01121 0.92372 0.38292 12.15180; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31166 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (134246) Reverse Loop had 15404 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 97074, nSrcLost = 0, nSrcMulti = 37172, MnSrcMultiHits = 2.21059 nTrg121 = 149670, nTrgMulti = 14172, MnTrgMultiHits = 2.08693 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.sm5.fsaverage.lh.nii.gz Dim: 163842 1 1 mri_vol2surf done mris_fwhm --s fsaverage --hemi lh --smooth-only --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.sm5.fsaverage.lh.nii.gz --fwhm 5 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.sm5.fsaverage.lh.nii.gz --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.lh.nii.gz --no-detrend fsaverage lh white Number of vertices 163842 Number of faces 327680 Total area 65417.000000 GroupSurface 82219.960938 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.lh.nii.gz Found 149955 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=18 Only smoothing, so saving and exiting now 1/1 20240801_dw204 007 lh --------- Tue Jun 17 16:13:27 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi lh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.sm5.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA -------- original matrix ----------- 0.99999 0.00199 0.00301 -0.75541; -0.00208 -0.36274 0.93189 -16.20432; -0.00295 0.93189 0.36274 12.02584; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31189 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/lh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (134246) Reverse Loop had 15404 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 97074, nSrcLost = 0, nSrcMulti = 37172, MnSrcMultiHits = 2.21059 nTrg121 = 149670, nTrgMulti = 14172, MnTrgMultiHits = 2.08693 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/lh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.sm5.fsaverage.lh.nii.gz Dim: 163842 1 1 mri_vol2surf done mris_fwhm --s fsaverage --hemi lh --smooth-only --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.sm5.fsaverage.lh.nii.gz --fwhm 5 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.sm5.fsaverage.lh.nii.gz --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.lh.nii.gz --no-detrend fsaverage lh white Number of vertices 163842 Number of faces 327680 Total area 65417.000000 GroupSurface 82219.960938 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.lh.nii.gz Found 149955 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=18 Only smoothing, so saving and exiting now 1/1 20240801_dw204 002 rh --------- Tue Jun 17 16:14:31 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.sm5.fsaverage.rh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA -------- original matrix ----------- -0.03510 0.99892 -0.03050 0.64655; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01602; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 89107 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (136090) Reverse Loop had 17088 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 99202, nSrcLost = 0, nSrcMulti = 36888, MnSrcMultiHits = 2.21557 nTrg121 = 148228, nTrgMulti = 15614, MnTrgMultiHits = 2.0944 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.sm5.fsaverage.rh.nii.gz Dim: 163842 1 1 mri_vol2surf done mris_fwhm --s fsaverage --hemi rh --smooth-only --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.sm5.fsaverage.rh.nii.gz --fwhm 5 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.sm5.fsaverage.rh.nii.gz --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.rh.nii.gz --no-detrend fsaverage rh white Number of vertices 163842 Number of faces 327680 Total area 65020.855469 GroupSurface 82167.578125 AvgVtxArea 0.396851 AvgVtxDist 0.717994 StdVtxDist 0.193570 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.fsaverage.rh.nii.gz Found 149926 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=18 Only smoothing, so saving and exiting now 1/1 20240801_dw204 003 rh --------- Tue Jun 17 16:14:35 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.sm5.fsaverage.rh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA -------- original matrix ----------- 0.99995 -0.00300 0.00925 -0.46384; -0.00971 -0.35421 0.93512 -14.17781; -0.00047 0.93516 0.35422 10.90227; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31374 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (136090) Reverse Loop had 17088 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 99202, nSrcLost = 0, nSrcMulti = 36888, MnSrcMultiHits = 2.21557 nTrg121 = 148228, nTrgMulti = 15614, MnTrgMultiHits = 2.0944 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.sm5.fsaverage.rh.nii.gz Dim: 163842 1 1 mri_vol2surf done mris_fwhm --s fsaverage --hemi rh --smooth-only --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.sm5.fsaverage.rh.nii.gz --fwhm 5 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.sm5.fsaverage.rh.nii.gz --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.rh.nii.gz --no-detrend fsaverage rh white Number of vertices 163842 Number of faces 327680 Total area 65020.855469 GroupSurface 82167.578125 AvgVtxArea 0.396851 AvgVtxDist 0.717994 StdVtxDist 0.193570 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.fsaverage.rh.nii.gz Found 149926 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=18 Only smoothing, so saving and exiting now 1/1 20240801_dw204 004 rh --------- Tue Jun 17 16:14:47 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.sm5.fsaverage.rh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA -------- original matrix ----------- 0.99988 0.00031 0.01560 -0.73119; -0.01437 -0.37068 0.92865 -13.70915; -0.00607 0.92876 0.37063 12.62407; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31450 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (136090) Reverse Loop had 17088 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 99202, nSrcLost = 0, nSrcMulti = 36888, MnSrcMultiHits = 2.21557 nTrg121 = 148228, nTrgMulti = 15614, MnTrgMultiHits = 2.0944 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.sm5.fsaverage.rh.nii.gz Dim: 163842 1 1 mri_vol2surf done mris_fwhm --s fsaverage --hemi rh --smooth-only --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.sm5.fsaverage.rh.nii.gz --fwhm 5 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.sm5.fsaverage.rh.nii.gz --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.rh.nii.gz --no-detrend fsaverage rh white Number of vertices 163842 Number of faces 327680 Total area 65020.855469 GroupSurface 82167.578125 AvgVtxArea 0.396851 AvgVtxDist 0.717994 StdVtxDist 0.193570 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.fsaverage.rh.nii.gz Found 149926 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=18 Only smoothing, so saving and exiting now 1/1 20240801_dw204 005 rh --------- Tue Jun 17 16:14:58 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.sm5.fsaverage.rh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA -------- original matrix ----------- 0.99994 0.00665 0.00842 -0.60532; -0.00548 -0.35819 0.93363 -16.52873; -0.00923 0.93363 0.35813 12.42865; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31487 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (136090) Reverse Loop had 17088 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 99202, nSrcLost = 0, nSrcMulti = 36888, MnSrcMultiHits = 2.21557 nTrg121 = 148228, nTrgMulti = 15614, MnTrgMultiHits = 2.0944 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.sm5.fsaverage.rh.nii.gz Dim: 163842 1 1 mri_vol2surf done mris_fwhm --s fsaverage --hemi rh --smooth-only --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.sm5.fsaverage.rh.nii.gz --fwhm 5 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.sm5.fsaverage.rh.nii.gz --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.rh.nii.gz --no-detrend fsaverage rh white Number of vertices 163842 Number of faces 327680 Total area 65020.855469 GroupSurface 82167.578125 AvgVtxArea 0.396851 AvgVtxDist 0.717994 StdVtxDist 0.193570 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.fsaverage.rh.nii.gz Found 149926 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=18 Only smoothing, so saving and exiting now 1/1 20240801_dw204 006 rh --------- Tue Jun 17 16:15:16 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.sm5.fsaverage.rh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA -------- original matrix ----------- 0.99990 0.00705 0.01226 -0.54247; -0.00863 -0.38302 0.92370 -16.86919; -0.01121 0.92372 0.38292 12.15180; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31292 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (136090) Reverse Loop had 17088 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 99202, nSrcLost = 0, nSrcMulti = 36888, MnSrcMultiHits = 2.21557 nTrg121 = 148228, nTrgMulti = 15614, MnTrgMultiHits = 2.0944 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.sm5.fsaverage.rh.nii.gz Dim: 163842 1 1 mri_vol2surf done mris_fwhm --s fsaverage --hemi rh --smooth-only --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.sm5.fsaverage.rh.nii.gz --fwhm 5 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.sm5.fsaverage.rh.nii.gz --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.rh.nii.gz --no-detrend fsaverage rh white Number of vertices 163842 Number of faces 327680 Total area 65020.855469 GroupSurface 82167.578125 AvgVtxArea 0.396851 AvgVtxDist 0.717994 StdVtxDist 0.193570 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.fsaverage.rh.nii.gz Found 149926 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=18 Only smoothing, so saving and exiting now 1/1 20240801_dw204 007 rh --------- Tue Jun 17 16:20:30 EDT 2025 mri_vol2surf --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.sm5.fsaverage.rh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.nii.gz srcreg = /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA -------- original matrix ----------- 0.99999 0.00199 0.00301 -0.75541; -0.00208 -0.36274 0.93189 -16.20432; -0.00295 0.93189 0.36274 12.02584; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Reading surface /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.white Done reading source surface Reading thickness /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface Projecting 0.5 0.5 1 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 31445 Reading source surface registration /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/surf/rh.sphere.reg Done loading source registration surface Reading target registration /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (20240801_dw204 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (136090) Reverse Loop had 17088 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 99202, nSrcLost = 0, nSrcMulti = 36888, MnSrcMultiHits = 2.21557 nTrg121 = 148228, nTrgMulti = 15614, MnTrgMultiHits = 2.0944 Masking with /Volumes/umms-hillmera/asem_ptsd/DW204/fsaverage/label/rh.cortex.label Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.sm5.fsaverage.rh.nii.gz Dim: 163842 1 1 mri_vol2surf done mris_fwhm --s fsaverage --hemi rh --smooth-only --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.sm5.fsaverage.rh.nii.gz --fwhm 5 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.sm5.fsaverage.rh.nii.gz --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.rh.nii.gz --no-detrend fsaverage rh white Number of vertices 163842 Number of faces 327680 Total area 65020.855469 GroupSurface 82167.578125 AvgVtxArea 0.396851 AvgVtxDist 0.717994 StdVtxDist 0.193570 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.fsaverage.rh.nii.gz Found 149926 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=18 Only smoothing, so saving and exiting now Tue Jun 17 16:21:51 EDT 2025 rawfunc2surf-sess completed 20240801_dw204 To MNI305 ----------------------------- rawfunc2tal-sess -fwhm 5 -s 20240801_dw204 -d /Volumes/umms-hillmera/asem_ptsd/DW204 -fsd bold -stc up -update -subcort-mask -per-run ------------------------------ 1/1 20240801_dw204 20240801_dw204 1/1 20240801_dw204 002 ---------------- Tue Jun 17 16:21:51 EDT 2025 mri_vol2vol --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/register.dof6.lta --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.mni305.2mm.pr.nii.gz regio_read_register: loading lta Matrix from regfile: -0.03510 0.99892 -0.03050 0.64655; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01603; 0.00000 0.00000 0.00000 1.00000; movvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.nii.gz targvol /Applications/freesurfer/average/mni305.cor.subfov2.mgz outvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.mni305.2mm.pr.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/register.dof6.lta invert 0 tal 1 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1751161914 Compute R for talairach space matrix from regfile ---------------------- -0.03510 0.99892 -0.03050 0.64655; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01603; 0.00000 0.00000 0.00000 1.00000; Xtal ---------------------- 1.11212 0.04614 -0.03198 2.25193; -0.02063 0.97999 0.41954 -4.18182; -0.00159 -0.30075 1.11499 1.50680; 0.00000 0.00000 0.00000 1.00000; Rtal ---------------------- 1.00000 0.00000 0.00000 2.00000; 0.00000 1.00000 0.00000 16.00000; 0.00000 0.00000 1.00000 -9.00000; 0.00000 0.00000 0.00000 1.00000; Final tkRAS-to-tkRAS Matrix is: -0.01526 0.90679 -0.36899 -12.77016; 0.89824 -0.00597 0.00431 4.82537; 0.02902 0.27427 0.79377 2.59914; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -0.03052 -0.73799 -1.81359 254.30551; 0.05803 1.58754 -0.54854 88.37627; -1.79648 -0.00862 -0.01194 161.97424; 0.00000 0.00000 0.00000 1.00000; Resampling mri_vol2vol done mri_mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.mni305.2mm.pr.nii.gz /Applications/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.mni305.2mm.pr.nii.gz error: freadFloat: fread failed DoAbs = 0 maskval=0, outval=0 Writing masked volume to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.mni305.2mm.pr.nii.gz...done. 1/1 20240801_dw204 003 ---------------- Tue Jun 17 16:21:52 EDT 2025 mri_vol2vol --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/register.dof6.lta --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.mni305.2mm.pr.nii.gz regio_read_register: loading lta Matrix from regfile: 0.99995 -0.00300 0.00925 -0.46387; -0.00971 -0.35421 0.93512 -14.17781; -0.00047 0.93516 0.35422 10.90225; 0.00000 0.00000 0.00000 1.00000; movvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.nii.gz targvol /Applications/freesurfer/average/mni305.cor.subfov2.mgz outvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.mni305.2mm.pr.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/register.dof6.lta invert 0 tal 1 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750942807 Compute R for talairach space matrix from regfile ---------------------- 0.99995 -0.00300 0.00925 -0.46387; -0.00971 -0.35421 0.93512 -14.17781; -0.00047 0.93516 0.35422 10.90225; 0.00000 0.00000 0.00000 1.00000; Xtal ---------------------- 1.11212 0.04614 -0.03198 2.25193; -0.02063 0.97999 0.41954 -4.18182; -0.00159 -0.30075 1.11499 1.50680; 0.00000 0.00000 0.00000 1.00000; Rtal ---------------------- 1.00000 0.00000 0.00000 2.00000; 0.00000 1.00000 0.00000 16.00000; 0.00000 0.00000 1.00000 -9.00000; 0.00000 0.00000 0.00000 1.00000; Final tkRAS-to-tkRAS Matrix is: 0.89863 -0.03130 0.04585 -3.57135; -0.00921 -0.09297 0.87340 -6.49536; 0.01701 0.94229 -0.03638 -0.57886; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 0.89863 0.04585 0.03130 19.44025; 0.01701 -0.03638 -0.94229 99.84225; 0.00921 -0.87340 -0.09297 65.91457; 0.00000 0.00000 0.00000 1.00000; Resampling mri_vol2vol done mri_mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.mni305.2mm.pr.nii.gz /Applications/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.mni305.2mm.pr.nii.gz error: freadFloat: fread failed DoAbs = 0 maskval=0, outval=0 Writing masked volume to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.mni305.2mm.pr.nii.gz...done. 1/1 20240801_dw204 004 ---------------- Tue Jun 17 16:21:52 EDT 2025 mri_vol2vol --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/register.dof6.lta --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.mni305.2mm.pr.nii.gz regio_read_register: loading lta Matrix from regfile: 0.99988 0.00031 0.01560 -0.73120; -0.01437 -0.37068 0.92865 -13.70918; -0.00607 0.92876 0.37063 12.62407; 0.00000 0.00000 0.00000 1.00000; movvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.nii.gz targvol /Applications/freesurfer/average/mni305.cor.subfov2.mgz outvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.mni305.2mm.pr.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/register.dof6.lta invert 0 tal 1 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750252475 Compute R for talairach space matrix from regfile ---------------------- 0.99988 0.00031 0.01560 -0.73120; -0.01437 -0.37068 0.92865 -13.70918; -0.00607 0.92876 0.37063 12.62407; 0.00000 0.00000 0.00000 1.00000; Xtal ---------------------- 1.11212 0.04614 -0.03198 2.25193; -0.02063 0.97999 0.41954 -4.18182; -0.00159 -0.30075 1.11499 1.50680; 0.00000 0.00000 0.00000 1.00000; Rtal ---------------------- 1.00000 0.00000 0.00000 2.00000; 0.00000 1.00000 0.00000 16.00000; 0.00000 0.00000 1.00000 -9.00000; 0.00000 0.00000 0.00000 1.00000; Final tkRAS-to-tkRAS Matrix is: 0.89865 -0.02671 0.04981 -3.86332; -0.01371 -0.10947 0.87368 -5.81046; 0.01197 0.94066 -0.02120 1.29746; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 0.89865 0.04981 0.02671 19.64811; 0.01197 -0.02120 -0.94066 98.44280; 0.01371 -0.87368 -0.10947 66.86432; 0.00000 0.00000 0.00000 1.00000; Resampling mri_vol2vol done mri_mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.mni305.2mm.pr.nii.gz /Applications/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.mni305.2mm.pr.nii.gz error: freadFloat: fread failed DoAbs = 0 maskval=0, outval=0 Writing masked volume to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.mni305.2mm.pr.nii.gz...done. 1/1 20240801_dw204 005 ---------------- Tue Jun 17 16:21:53 EDT 2025 mri_vol2vol --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/register.dof6.lta --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.mni305.2mm.pr.nii.gz regio_read_register: loading lta Matrix from regfile: 0.99994 0.00665 0.00842 -0.60532; -0.00548 -0.35819 0.93363 -16.52873; -0.00923 0.93363 0.35813 12.42867; 0.00000 0.00000 0.00000 1.00000; movvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.nii.gz targvol /Applications/freesurfer/average/mni305.cor.subfov2.mgz outvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.mni305.2mm.pr.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/register.dof6.lta invert 0 tal 1 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750572329 Compute R for talairach space matrix from regfile ---------------------- 0.99994 0.00665 0.00842 -0.60532; -0.00548 -0.35819 0.93363 -16.52873; -0.00923 0.93363 0.35813 12.42867; 0.00000 0.00000 0.00000 1.00000; Xtal ---------------------- 1.11212 0.04614 -0.03198 2.25193; -0.02063 0.97999 0.41954 -4.18182; -0.00159 -0.30075 1.11499 1.50680; 0.00000 0.00000 0.00000 1.00000; Rtal ---------------------- 1.00000 0.00000 0.00000 2.00000; 0.00000 1.00000 0.00000 16.00000; 0.00000 0.00000 1.00000 -9.00000; 0.00000 0.00000 0.00000 1.00000; Final tkRAS-to-tkRAS Matrix is: 0.89877 -0.02267 0.04187 -3.84515; -0.00548 -0.09710 0.87373 -8.81079; 0.00913 0.94212 -0.03304 1.00811; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 0.89877 0.04187 0.02267 20.12385; 0.00913 -0.03304 -0.94212 99.21302; 0.00548 -0.87373 -0.09710 63.10331; 0.00000 0.00000 0.00000 1.00000; Resampling mri_vol2vol done mri_mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.mni305.2mm.pr.nii.gz /Applications/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.mni305.2mm.pr.nii.gz error: freadFloat: fread failed DoAbs = 0 maskval=0, outval=0 Writing masked volume to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.mni305.2mm.pr.nii.gz...done. 1/1 20240801_dw204 006 ---------------- Tue Jun 17 16:21:53 EDT 2025 mri_vol2vol --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/register.dof6.lta --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.mni305.2mm.pr.nii.gz regio_read_register: loading lta Matrix from regfile: 0.99990 0.00705 0.01226 -0.54247; -0.00863 -0.38302 0.92370 -16.86917; -0.01121 0.92371 0.38292 12.15179; 0.00000 0.00000 0.00000 1.00000; movvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.nii.gz targvol /Applications/freesurfer/average/mni305.cor.subfov2.mgz outvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.mni305.2mm.pr.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/register.dof6.lta invert 0 tal 1 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750889988 Compute R for talairach space matrix from regfile ---------------------- 0.99990 0.00705 0.01226 -0.54247; -0.00863 -0.38302 0.92370 -16.86917; -0.01121 0.92371 0.38292 12.15179; 0.00000 0.00000 0.00000 1.00000; Xtal ---------------------- 1.11212 0.04614 -0.03198 2.25193; -0.02063 0.97999 0.41954 -4.18182; -0.00159 -0.30075 1.11499 1.50680; 0.00000 0.00000 0.00000 1.00000; Rtal ---------------------- 1.00000 0.00000 0.00000 2.00000; 0.00000 1.00000 0.00000 16.00000; 0.00000 0.00000 1.00000 -9.00000; 0.00000 0.00000 0.00000 1.00000; Final tkRAS-to-tkRAS Matrix is: 0.89876 -0.02136 0.04482 -3.77568; -0.00877 -0.12215 0.87415 -8.83802; 0.00733 0.93923 -0.00978 0.94736; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 0.89876 0.04482 0.02136 20.03853; 0.00733 -0.00978 -0.93923 98.29359; 0.00877 -0.87415 -0.12215 64.14549; 0.00000 0.00000 0.00000 1.00000; Resampling mri_vol2vol done mri_mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.mni305.2mm.pr.nii.gz /Applications/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.mni305.2mm.pr.nii.gz error: freadFloat: fread failed DoAbs = 0 maskval=0, outval=0 Writing masked volume to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.mni305.2mm.pr.nii.gz...done. 1/1 20240801_dw204 007 ---------------- Tue Jun 17 16:21:53 EDT 2025 mri_vol2vol --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/register.dof6.lta --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.mni305.2mm.pr.nii.gz regio_read_register: loading lta Matrix from regfile: 0.99999 0.00199 0.00301 -0.75541; -0.00208 -0.36274 0.93189 -16.20432; -0.00295 0.93189 0.36274 12.02583; 0.00000 0.00000 0.00000 1.00000; movvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.nii.gz targvol /Applications/freesurfer/average/mni305.cor.subfov2.mgz outvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.mni305.2mm.pr.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/register.dof6.lta invert 0 tal 1 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1751190043 Compute R for talairach space matrix from regfile ---------------------- 0.99999 0.00199 0.00301 -0.75541; -0.00208 -0.36274 0.93189 -16.20432; -0.00295 0.93189 0.36274 12.02583; 0.00000 0.00000 0.00000 1.00000; Xtal ---------------------- 1.11212 0.04614 -0.03198 2.25193; -0.02063 0.97999 0.41954 -4.18182; -0.00159 -0.30075 1.11499 1.50680; 0.00000 0.00000 0.00000 1.00000; Rtal ---------------------- 1.00000 0.00000 0.00000 2.00000; 0.00000 1.00000 0.00000 16.00000; 0.00000 0.00000 1.00000 -9.00000; 0.00000 0.00000 0.00000 1.00000; Final tkRAS-to-tkRAS Matrix is: 0.89871 -0.02827 0.03912 -3.94940; -0.00251 -0.10180 0.87402 -8.44131; 0.01478 0.94147 -0.02850 0.62292; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 0.89871 0.03912 0.02827 20.02246; 0.01478 -0.02850 -0.94147 98.98859; 0.00251 -0.87402 -0.10180 63.63042; 0.00000 0.00000 0.00000 1.00000; Resampling mri_vol2vol done mri_mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.mni305.2mm.pr.nii.gz /Applications/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.mni305.2mm.pr.nii.gz error: freadFloat: fread failed DoAbs = 0 maskval=0, outval=0 Writing masked volume to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.mni305.2mm.pr.nii.gz...done. mri_concat --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.mni305.2mm.nii.gz --mean /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.mni305.2mm.pr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.mni305.2mm.pr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.mni305.2mm.pr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.mni305.2mm.pr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.mni305.2mm.pr.nii.gz /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.mni305.2mm.pr.nii.gz ninputs = 6 Checking inputs nframestot = 6 Allocing output Done allocing nframes = 6 Computing mean across frames Writing to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.mni305.2mm.nii.gz mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.mni305.2mm.nii.gz --min 10e-10 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.mni305.2mm.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DW204 cmdline mri_binarize --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.mni305.2mm.nii.gz --min 10e-10 --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.mni305.2mm.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.mni305.2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.mni305.2mm.nii.gz Binarizing based on threshold min 1e-09 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 56311 values in range Counting number of voxels in first frame Found 56310 voxels in final mask Writing output to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/masks/brain.mni305.2mm.nii.gz Count: 56310 450480.000000 537168 10.482754 mri_binarize done 1/1 20240801_dw204 002 ---------------- Tue Jun 17 16:21:54 EDT 2025 mri_vol2vol --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/register.dof6.lta --tal --talres 2 --talxfm talairach.xfm --interp trilin --no-save-reg --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.sm5.mni305.2mm.nii.gz regio_read_register: loading lta Matrix from regfile: -0.03510 0.99892 -0.03050 0.64655; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01603; 0.00000 0.00000 0.00000 1.00000; movvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.nii.gz targvol /Applications/freesurfer/average/mni305.cor.subfov2.mgz outvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.sm5.mni305.2mm.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/register.dof6.lta invert 0 tal 1 talres 2 regheader 0 noresample 0 interp trilin (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750238864 Compute R for talairach space matrix from regfile ---------------------- -0.03510 0.99892 -0.03050 0.64655; 0.99906 0.03430 -0.02643 8.54176; 0.02535 0.03139 0.99919 0.01603; 0.00000 0.00000 0.00000 1.00000; Xtal ---------------------- 1.11212 0.04614 -0.03198 2.25193; -0.02063 0.97999 0.41954 -4.18182; -0.00159 -0.30075 1.11499 1.50680; 0.00000 0.00000 0.00000 1.00000; Rtal ---------------------- 1.00000 0.00000 0.00000 2.00000; 0.00000 1.00000 0.00000 16.00000; 0.00000 0.00000 1.00000 -9.00000; 0.00000 0.00000 0.00000 1.00000; Final tkRAS-to-tkRAS Matrix is: -0.01526 0.90679 -0.36899 -12.77016; 0.89824 -0.00597 0.00431 4.82537; 0.02902 0.27427 0.79377 2.59914; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -0.03052 -0.73799 -1.81359 254.30551; 0.05803 1.58754 -0.54854 88.37627; -1.79648 -0.00862 -0.01194 161.97424; 0.00000 0.00000 0.00000 1.00000; Resampling mri_vol2vol done mri_fwhm --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.sm5.mni305.2mm.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.sm5.mni305.2mm.nii.gz --smooth-only --fwhm 5 --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.mni305.2mm.nii.gz voxelvolume 8 mm3 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/masks/brain.mni305.2mm.nii.gz Search region is 56311 voxels = 450488.000000 mm3 Smoothing input by fwhm=5.000000, gstd=2.123305 Saving to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/002/fmcpr.up.sm5.mni305.2mm.nii.gz SmoothOnly requested, so exiting now 1/1 20240801_dw204 003 ---------------- Tue Jun 17 16:21:55 EDT 2025 mri_vol2vol --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/register.dof6.lta --tal --talres 2 --talxfm talairach.xfm --interp trilin --no-save-reg --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.sm5.mni305.2mm.nii.gz regio_read_register: loading lta Matrix from regfile: 0.99995 -0.00300 0.00925 -0.46387; -0.00971 -0.35421 0.93512 -14.17781; -0.00047 0.93516 0.35422 10.90225; 0.00000 0.00000 0.00000 1.00000; movvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.nii.gz targvol /Applications/freesurfer/average/mni305.cor.subfov2.mgz outvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.sm5.mni305.2mm.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/register.dof6.lta invert 0 tal 1 talres 2 regheader 0 noresample 0 interp trilin (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750760144 Compute R for talairach space matrix from regfile ---------------------- 0.99995 -0.00300 0.00925 -0.46387; -0.00971 -0.35421 0.93512 -14.17781; -0.00047 0.93516 0.35422 10.90225; 0.00000 0.00000 0.00000 1.00000; Xtal ---------------------- 1.11212 0.04614 -0.03198 2.25193; -0.02063 0.97999 0.41954 -4.18182; -0.00159 -0.30075 1.11499 1.50680; 0.00000 0.00000 0.00000 1.00000; Rtal ---------------------- 1.00000 0.00000 0.00000 2.00000; 0.00000 1.00000 0.00000 16.00000; 0.00000 0.00000 1.00000 -9.00000; 0.00000 0.00000 0.00000 1.00000; Final tkRAS-to-tkRAS Matrix is: 0.89863 -0.03130 0.04585 -3.57135; -0.00921 -0.09297 0.87340 -6.49536; 0.01701 0.94229 -0.03638 -0.57886; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 0.89863 0.04585 0.03130 19.44025; 0.01701 -0.03638 -0.94229 99.84225; 0.00921 -0.87340 -0.09297 65.91457; 0.00000 0.00000 0.00000 1.00000; Resampling mri_vol2vol done mri_fwhm --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.sm5.mni305.2mm.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.sm5.mni305.2mm.nii.gz --smooth-only --fwhm 5 --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.mni305.2mm.nii.gz voxelvolume 8 mm3 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/masks/brain.mni305.2mm.nii.gz Search region is 56311 voxels = 450488.000000 mm3 Smoothing input by fwhm=5.000000, gstd=2.123305 Saving to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/003/fmcpr.up.sm5.mni305.2mm.nii.gz SmoothOnly requested, so exiting now 1/1 20240801_dw204 004 ---------------- Tue Jun 17 16:22:26 EDT 2025 mri_vol2vol --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/register.dof6.lta --tal --talres 2 --talxfm talairach.xfm --interp trilin --no-save-reg --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.sm5.mni305.2mm.nii.gz regio_read_register: loading lta Matrix from regfile: 0.99988 0.00031 0.01560 -0.73120; -0.01437 -0.37068 0.92865 -13.70918; -0.00607 0.92876 0.37063 12.62407; 0.00000 0.00000 0.00000 1.00000; movvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.nii.gz targvol /Applications/freesurfer/average/mni305.cor.subfov2.mgz outvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.sm5.mni305.2mm.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/register.dof6.lta invert 0 tal 1 talres 2 regheader 0 noresample 0 interp trilin (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750539754 Compute R for talairach space matrix from regfile ---------------------- 0.99988 0.00031 0.01560 -0.73120; -0.01437 -0.37068 0.92865 -13.70918; -0.00607 0.92876 0.37063 12.62407; 0.00000 0.00000 0.00000 1.00000; Xtal ---------------------- 1.11212 0.04614 -0.03198 2.25193; -0.02063 0.97999 0.41954 -4.18182; -0.00159 -0.30075 1.11499 1.50680; 0.00000 0.00000 0.00000 1.00000; Rtal ---------------------- 1.00000 0.00000 0.00000 2.00000; 0.00000 1.00000 0.00000 16.00000; 0.00000 0.00000 1.00000 -9.00000; 0.00000 0.00000 0.00000 1.00000; Final tkRAS-to-tkRAS Matrix is: 0.89865 -0.02671 0.04981 -3.86332; -0.01371 -0.10947 0.87368 -5.81046; 0.01197 0.94066 -0.02120 1.29746; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 0.89865 0.04981 0.02671 19.64811; 0.01197 -0.02120 -0.94066 98.44280; 0.01371 -0.87368 -0.10947 66.86432; 0.00000 0.00000 0.00000 1.00000; Resampling mri_vol2vol done mri_fwhm --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.sm5.mni305.2mm.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.sm5.mni305.2mm.nii.gz --smooth-only --fwhm 5 --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.mni305.2mm.nii.gz voxelvolume 8 mm3 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/masks/brain.mni305.2mm.nii.gz Search region is 56311 voxels = 450488.000000 mm3 Smoothing input by fwhm=5.000000, gstd=2.123305 Saving to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/004/fmcpr.up.sm5.mni305.2mm.nii.gz SmoothOnly requested, so exiting now 1/1 20240801_dw204 005 ---------------- Tue Jun 17 16:23:08 EDT 2025 mri_vol2vol --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/register.dof6.lta --tal --talres 2 --talxfm talairach.xfm --interp trilin --no-save-reg --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.sm5.mni305.2mm.nii.gz regio_read_register: loading lta Matrix from regfile: 0.99994 0.00665 0.00842 -0.60532; -0.00548 -0.35819 0.93363 -16.52873; -0.00923 0.93363 0.35813 12.42867; 0.00000 0.00000 0.00000 1.00000; movvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.nii.gz targvol /Applications/freesurfer/average/mni305.cor.subfov2.mgz outvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.sm5.mni305.2mm.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/register.dof6.lta invert 0 tal 1 talres 2 regheader 0 noresample 0 interp trilin (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750591210 Compute R for talairach space matrix from regfile ---------------------- 0.99994 0.00665 0.00842 -0.60532; -0.00548 -0.35819 0.93363 -16.52873; -0.00923 0.93363 0.35813 12.42867; 0.00000 0.00000 0.00000 1.00000; Xtal ---------------------- 1.11212 0.04614 -0.03198 2.25193; -0.02063 0.97999 0.41954 -4.18182; -0.00159 -0.30075 1.11499 1.50680; 0.00000 0.00000 0.00000 1.00000; Rtal ---------------------- 1.00000 0.00000 0.00000 2.00000; 0.00000 1.00000 0.00000 16.00000; 0.00000 0.00000 1.00000 -9.00000; 0.00000 0.00000 0.00000 1.00000; Final tkRAS-to-tkRAS Matrix is: 0.89877 -0.02267 0.04187 -3.84515; -0.00548 -0.09710 0.87373 -8.81079; 0.00913 0.94212 -0.03304 1.00811; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 0.89877 0.04187 0.02267 20.12385; 0.00913 -0.03304 -0.94212 99.21302; 0.00548 -0.87373 -0.09710 63.10331; 0.00000 0.00000 0.00000 1.00000; Resampling mri_vol2vol done mri_fwhm --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.sm5.mni305.2mm.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.sm5.mni305.2mm.nii.gz --smooth-only --fwhm 5 --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.mni305.2mm.nii.gz voxelvolume 8 mm3 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/masks/brain.mni305.2mm.nii.gz Search region is 56311 voxels = 450488.000000 mm3 Smoothing input by fwhm=5.000000, gstd=2.123305 Saving to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/005/fmcpr.up.sm5.mni305.2mm.nii.gz SmoothOnly requested, so exiting now 1/1 20240801_dw204 006 ---------------- Tue Jun 17 16:23:41 EDT 2025 mri_vol2vol --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/register.dof6.lta --tal --talres 2 --talxfm talairach.xfm --interp trilin --no-save-reg --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.sm5.mni305.2mm.nii.gz regio_read_register: loading lta Matrix from regfile: 0.99990 0.00705 0.01226 -0.54247; -0.00863 -0.38302 0.92370 -16.86917; -0.01121 0.92371 0.38292 12.15179; 0.00000 0.00000 0.00000 1.00000; movvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.nii.gz targvol /Applications/freesurfer/average/mni305.cor.subfov2.mgz outvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.sm5.mni305.2mm.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/register.dof6.lta invert 0 tal 1 talres 2 regheader 0 noresample 0 interp trilin (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750619125 Compute R for talairach space matrix from regfile ---------------------- 0.99990 0.00705 0.01226 -0.54247; -0.00863 -0.38302 0.92370 -16.86917; -0.01121 0.92371 0.38292 12.15179; 0.00000 0.00000 0.00000 1.00000; Xtal ---------------------- 1.11212 0.04614 -0.03198 2.25193; -0.02063 0.97999 0.41954 -4.18182; -0.00159 -0.30075 1.11499 1.50680; 0.00000 0.00000 0.00000 1.00000; Rtal ---------------------- 1.00000 0.00000 0.00000 2.00000; 0.00000 1.00000 0.00000 16.00000; 0.00000 0.00000 1.00000 -9.00000; 0.00000 0.00000 0.00000 1.00000; Final tkRAS-to-tkRAS Matrix is: 0.89876 -0.02136 0.04482 -3.77568; -0.00877 -0.12215 0.87415 -8.83802; 0.00733 0.93923 -0.00978 0.94736; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 0.89876 0.04482 0.02136 20.03853; 0.00733 -0.00978 -0.93923 98.29359; 0.00877 -0.87415 -0.12215 64.14549; 0.00000 0.00000 0.00000 1.00000; Resampling mri_vol2vol done mri_fwhm --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.sm5.mni305.2mm.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.sm5.mni305.2mm.nii.gz --smooth-only --fwhm 5 --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.mni305.2mm.nii.gz voxelvolume 8 mm3 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/masks/brain.mni305.2mm.nii.gz Search region is 56311 voxels = 450488.000000 mm3 Smoothing input by fwhm=5.000000, gstd=2.123305 Saving to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/006/fmcpr.up.sm5.mni305.2mm.nii.gz SmoothOnly requested, so exiting now 1/1 20240801_dw204 007 ---------------- Tue Jun 17 16:42:27 EDT 2025 mri_vol2vol --mov /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/register.dof6.lta --tal --talres 2 --talxfm talairach.xfm --interp trilin --no-save-reg --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.sm5.mni305.2mm.nii.gz regio_read_register: loading lta Matrix from regfile: 0.99999 0.00199 0.00301 -0.75541; -0.00208 -0.36274 0.93189 -16.20432; -0.00295 0.93189 0.36274 12.02583; 0.00000 0.00000 0.00000 1.00000; movvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.nii.gz targvol /Applications/freesurfer/average/mni305.cor.subfov2.mgz outvol /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.sm5.mni305.2mm.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/register.dof6.lta invert 0 tal 1 talres 2 regheader 0 noresample 0 interp trilin (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1751062461 Compute R for talairach space matrix from regfile ---------------------- 0.99999 0.00199 0.00301 -0.75541; -0.00208 -0.36274 0.93189 -16.20432; -0.00295 0.93189 0.36274 12.02583; 0.00000 0.00000 0.00000 1.00000; Xtal ---------------------- 1.11212 0.04614 -0.03198 2.25193; -0.02063 0.97999 0.41954 -4.18182; -0.00159 -0.30075 1.11499 1.50680; 0.00000 0.00000 0.00000 1.00000; Rtal ---------------------- 1.00000 0.00000 0.00000 2.00000; 0.00000 1.00000 0.00000 16.00000; 0.00000 0.00000 1.00000 -9.00000; 0.00000 0.00000 0.00000 1.00000; Final tkRAS-to-tkRAS Matrix is: 0.89871 -0.02827 0.03912 -3.94940; -0.00251 -0.10180 0.87402 -8.44131; 0.01478 0.94147 -0.02850 0.62292; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 0.89871 0.03912 0.02827 20.02246; 0.01478 -0.02850 -0.94147 98.98859; 0.00251 -0.87402 -0.10180 63.63042; 0.00000 0.00000 0.00000 1.00000; Resampling mri_vol2vol done mri_fwhm --i /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.sm5.mni305.2mm.nii.gz --o /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.sm5.mni305.2mm.nii.gz --smooth-only --fwhm 5 --mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.mni305.2mm.nii.gz voxelvolume 8 mm3 Loading mask /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/masks/brain.mni305.2mm.nii.gz Search region is 56311 voxels = 450488.000000 mm3 Smoothing input by fwhm=5.000000, gstd=2.123305 Saving to /Volumes/umms-hillmera/asem_ptsd/DW204/20240801_dw204/bold/007/fmcpr.up.sm5.mni305.2mm.nii.gz SmoothOnly requested, so exiting now Tue Jun 17 16:44:53 EDT 2025 rawfunc2tal-sess completed ---------------------------------------- Started at Tue Jun 17 14:00:48 EDT 2025 Ended at Tue Jun 17 16:44:53 EDT 2025 preproc-sess done (base) hibahmch@mac-mvqmt7cvdq DW204 % cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 (base) hibahmch@mac-mvqmt7cvdq 20231006_da047 % cd 3d_dicom_orig (base) hibahmch@mac-mvqmt7cvdq 3d_dicom_orig % dcmunpack -src . -index-out dcm.index.dat cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig /Applications/freesurfer/bin/dcmunpack -src . -index-out dcm.index.dat -rwxr-xr-x 1 hibahmch wheel 36797 Jun 14 2023 /Applications/freesurfer/bin/dcmunpack --------------------------------------- --------------------------------------- Searching for matching files Wed Jun 18 09:24:50 EDT 2025 Wed Jun 18 09:24:51 EDT 2025 Found 2027 total files. Interrogating each and every one of them. Be patient. Found 7 unique series: 1 2 3 4 5 6 7 Subject reversal Date 20231006 Time 080905.622000 Institution Yale University School of Medicine 1 localizer 5 20 40 0.546875\0.546875 COL 180 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608243294541229542 2 Sag_3D_MPRAGE_10_05 2.81 2530 7 unknown ROW 180 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608332712301130724 3 cmrr_mbep2d_diff_AP 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608360981194938784 4 cmrr_mbep2d_diff_PA 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608403236423463966 5 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202310060856478755775641 6 cmrr_mbep2d_boldMB4iPAT2 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100609054141847134421 7 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202310060925148773331558 Wed Jun 18 09:43:17 EDT 2025 dcmunpack done (base) hibahmch@mac-mvqmt7cvdq 3d_dicom_orig % dcmunpack -src . -index-in dcm.index.dat -targ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 \ > -run 2 bold nii f.nii \ > -run 3 bold nii f.nii \ > -run 4 bold nii f.nii \ > -run 5 bold nii f.nii \ > -run 6 bold nii f.nii \ > -run 7 bold nii f.nii cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig /Applications/freesurfer/bin/dcmunpack -src . -index-in dcm.index.dat -targ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 -run 2 bold nii f.nii -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -rwxr-xr-x 1 hibahmch wheel 36797 Jun 14 2023 /Applications/freesurfer/bin/dcmunpack --------------------------------------- 1 2 bold f 0 0 2 3 bold f 0 0 3 4 bold f 0 0 4 5 bold f 0 0 5 6 bold f 0 0 6 7 bold f 0 0 --------------------------------------- Searching for matching files Wed Jun 18 09:48:25 EDT 2025 Wed Jun 18 09:48:26 EDT 2025 Found 2027 total files. Found 7 unique series: 1 2 3 4 5 6 7 Subject reversal Date 20231006 Time 080905.622000 Institution Yale University School of Medicine 1 localizer 5 20 40 0.546875\0.546875 COL 180 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608243294541229542 2 Sag_3D_MPRAGE_10_05 2.81 2530 7 unknown ROW 180 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608332712301130724 3 cmrr_mbep2d_diff_AP 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608360981194938784 4 cmrr_mbep2d_diff_PA 95 2369 90 unknown COL 1820 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608403236423463966 5 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202310060856478755775641 6 cmrr_mbep2d_boldMB4iPAT2 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100609054141847134421 7 cmrr_mbep2d_boldMB4iPAT2-rest 30 1000 60 unknown COL 1750 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202310060925148773331558 #@# Run 2 Wed Jun 18 09:48:27 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608332712301130724 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608332712301130724 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608332712301130724... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608332712301130724 dcmdir = /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/. Found 2025 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608332893028430784, size 131072 Convert 176 DICOM (256x256x176x1) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms TR=2530.00, TE=2.81, TI=1100.00, flip angle=7.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/f.nii... #@# Run 3 Wed Jun 18 09:49:38 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608360981194938784 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608360981194938784 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608360981194938784... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608360981194938784 dcmdir = /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/. Found 2025 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608351086236431968, size 1548800 Check Siemens/Philips bvecs: expected Patient Position (0018,5100) to be 'HFS' not 'HFS' Convert 65 DICOM (110x110x64x65) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. IsDWI = 1, IsPhilipsDWI = 0 TR=2369.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) writing to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/f.nii... Saving bvals and bvecs #@# Run 4 Wed Jun 18 09:50:49 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608403236423463966 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608403236423463966 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608403236423463966... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608403236423463966 dcmdir = /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/. Found 2025 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608381719533248874, size 1548800 Check Siemens/Philips bvecs: expected Patient Position (0018,5100) to be 'HFS' not 'HFS' Convert 65 DICOM (110x110x64x65) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. IsDWI = 1, IsPhilipsDWI = 0 TR=2369.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) writing to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/f.nii... Saving bvals and bvecs #@# Run 5 Wed Jun 18 09:52:02 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202310060856478755775641 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202310060856478755775641 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202310060856478755775641... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202310060856478755775641 dcmdir = /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/. Found 2025 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100608555577077166156, size 1452000 Convert 100 DICOM (110x110x60x100) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) writing to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/f.nii... #@# Run 6 Wed Jun 18 09:53:17 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100609054141847134421 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100609054141847134421 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100609054141847134421... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100609054141847134421 dcmdir = /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/. Found 2025 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.2023100609011156259984537, size 1452000 Convert 1156 DICOM (110x110x60x1156) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) writing to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/f.nii... #@# Run 7 Wed Jun 18 09:55:56 EDT 2025 ================================== mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202310060925148773331558 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/007/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202310060925148773331558 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/007/f.nii --nskip 0 --ndrop 0 -dcm2niix -no-siemensBVecsCross nskip = 0 ndrop = 0 reading from /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202310060925148773331558... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202310060925148773331558 dcmdir = /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/. Found 2025 DICOM file(s) load Image /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/3d_dicom_orig/./MR.1.3.12.2.1107.5.2.43.67084.202310060921549403095048, size 1452000 Convert 460 DICOM (110x110x60x460) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms INFO: This is an unsigned short. TR=1000.00, TE=30.00, TI=-1.00, flip angle=60.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) writing to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/007/f.nii... Started at Wed Jun 18 09:48:25 EDT 2025 Ended at Wed Jun 18 09:57:23 EDT 2025 dcmunpack-Run-Time-Min 8.97 Wed Jun 18 09:57:23 EDT 2025 dcmunpack done (base) hibahmch@mac-mvqmt7cvdq 3d_dicom_orig % cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 (base) hibahmch@mac-mvqmt7cvdq 20231006_da047 % touch subjectname.txt (base) hibahmch@mac-mvqmt7cvdq 20231006_da047 % export SUBJECTS_DIR=/Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 (base) hibahmch@mac-mvqmt7cvdq 20231006_da047 % cd /Volumes/umms-hillmera/asem_ptsd/DA047 (base) hibahmch@mac-mvqmt7cvdq DA047 % preproc-sess -s 20231006_da047 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run ERROR: cannot find fsaverage in /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 (base) hibahmch@mac-mvqmt7cvdq DA047 % preproc-sess -s 20231006_da047 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.20231006_da047.log -------------------------------------------------------------- FreeSurferEnv.csh 7.4.1 hibahmch setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 /Volumes/umms-hillmera/asem_ptsd/DA047 /Applications/freesurfer/fsfast/bin/preproc-sess -s 20231006_da047 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Wed Jun 18 10:01:49 EDT 2025 instem f mc 1 f fmcpr stc 1 fmcpr fmcpr.up sm 0 mask 1 brain 20231006_da047 Template ----------------------------- mktemplate-sess -s 20231006_da047 -d /Volumes/umms-hillmera/asem_ptsd/DA047 -fsd bold -funcstem f -update Session: /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 ---------------- Wed Jun 18 10:01:50 EDT 2025 Detected input format at nii /Volumes/umms-hillmera/asem_ptsd/DA047 mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/f.nii /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/template.nii.gz --frame 0 mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/f.nii /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/template.nii.gz --frame 0 reading from /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/f.nii... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) keeping frame 0 writing to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/template.nii.gz... Run: 002 ---------------- Wed Jun 18 10:01:52 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DA047 mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/f.nii /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/template.nii.gz --mid-frame mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/f.nii /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/template.nii.gz --mid-frame reading from /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/f.nii... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) keeping frame 0 writing to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/template.nii.gz... Run: 003 ---------------- Wed Jun 18 10:01:53 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DA047 mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/f.nii /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/template.nii.gz --mid-frame mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/f.nii /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/template.nii.gz --mid-frame reading from /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/f.nii... INFO: This is an unsigined short. TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) keeping frame 32 writing to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/template.nii.gz... Run: 004 ---------------- Wed Jun 18 10:01:56 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DA047 mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/f.nii /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/template.nii.gz --mid-frame mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/f.nii /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/template.nii.gz --mid-frame reading from /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/f.nii... INFO: This is an unsigined short. TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) keeping frame 32 writing to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/template.nii.gz... Run: 005 ---------------- Wed Jun 18 10:01:58 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DA047 mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/f.nii /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/template.nii.gz --mid-frame mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/f.nii /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/template.nii.gz --mid-frame reading from /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/f.nii... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) keeping frame 50 writing to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/template.nii.gz... Run: 006 ---------------- Wed Jun 18 10:02:01 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DA047 mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/f.nii /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/template.nii.gz --mid-frame mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/f.nii /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/template.nii.gz --mid-frame ^C (base) hibahmch@mac-mvqmt7cvdq DA047 % preproc-sess -s 20231006_da047 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.20231006_da047.log -------------------------------------------------------------- FreeSurferEnv.csh 7.4.1 hibahmch setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 /Volumes/umms-hillmera/asem_ptsd/DA047 /Applications/freesurfer/fsfast/bin/preproc-sess -s 20231006_da047 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Wed Jun 18 10:02:26 EDT 2025 instem f mc 1 f fmcpr stc 1 fmcpr fmcpr.up sm 0 mask 1 brain 20231006_da047 Template ----------------------------- mktemplate-sess -s 20231006_da047 -d /Volumes/umms-hillmera/asem_ptsd/DA047 -fsd bold -funcstem f -update Session: /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 ---------------- Wed Jun 18 10:02:27 EDT 2025 Detected input format at nii 20231006_da047 Update not needed Run: 002 ---------------- Wed Jun 18 10:02:27 EDT 2025 20231006_da047 002 Update not needed Run: 003 ---------------- Wed Jun 18 10:02:27 EDT 2025 20231006_da047 003 Update not needed Run: 004 ---------------- Wed Jun 18 10:02:27 EDT 2025 20231006_da047 004 Update not needed Run: 005 ---------------- Wed Jun 18 10:02:27 EDT 2025 20231006_da047 005 Update not needed Run: 006 ---------------- Wed Jun 18 10:02:27 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DA047 mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/f.nii /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/template.nii.gz --mid-frame mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/f.nii /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/template.nii.gz --mid-frame reading from /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/f.nii... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) keeping frame 578 writing to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/template.nii.gz... Run: 007 ---------------- Wed Jun 18 10:04:15 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DA047 mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/007/f.nii /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/007/template.nii.gz --mid-frame mri_convert /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/007/f.nii /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/007/template.nii.gz --mid-frame reading from /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/007/f.nii... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) keeping frame 230 writing to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/007/template.nii.gz... Wed Jun 18 10:04:29 EDT 2025 mktemplate-sess completed 20231006_da047 Registration ----------------------------- register-sess -s 20231006_da047 -d /Volumes/umms-hillmera/asem_ptsd/DA047 -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg -------------------------------------------------------------- register-sess logfile is /Volumes/umms-hillmera/asem_ptsd/DA047/log/register-sess.20231006_da047.log -------------------------------------------------------------- Wed Jun 18 10:04:29 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 cd /Volumes/umms-hillmera/asem_ptsd/DA047 /Applications/freesurfer/fsfast/bin/register-sess -s 20231006_da047 -d /Volumes/umms-hillmera/asem_ptsd/DA047 -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 Session: /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 ---------------- Wed Jun 18 10:04:29 EDT 2025 ERROR: 20231006_da047 is not in SUBJECTS_DIR SUBJECTS_DIR is /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 (base) hibahmch@mac-mvqmt7cvdq DA047 % export SUBJECTS_DIR=/Volumes/umms-hillmera/asem_ptsd/DA047 (base) hibahmch@mac-mvqmt7cvdq DA047 % preproc-sess -s 20231006_da047 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.20231006_da047.log -------------------------------------------------------------- FreeSurferEnv.csh 7.4.1 hibahmch setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 /Volumes/umms-hillmera/asem_ptsd/DA047 /Applications/freesurfer/fsfast/bin/preproc-sess -s 20231006_da047 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Wed Jun 18 10:05:04 EDT 2025 instem f mc 1 f fmcpr stc 1 fmcpr fmcpr.up sm 0 mask 1 brain 20231006_da047 Template ----------------------------- mktemplate-sess -s 20231006_da047 -d /Volumes/umms-hillmera/asem_ptsd/DA047 -fsd bold -funcstem f -update Session: /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 ---------------- Wed Jun 18 10:05:05 EDT 2025 Detected input format at nii 20231006_da047 Update not needed Run: 002 ---------------- Wed Jun 18 10:05:05 EDT 2025 20231006_da047 002 Update not needed Run: 003 ---------------- Wed Jun 18 10:05:05 EDT 2025 20231006_da047 003 Update not needed Run: 004 ---------------- Wed Jun 18 10:05:05 EDT 2025 20231006_da047 004 Update not needed Run: 005 ---------------- Wed Jun 18 10:05:05 EDT 2025 20231006_da047 005 Update not needed Run: 006 ---------------- Wed Jun 18 10:05:06 EDT 2025 20231006_da047 006 Update not needed Run: 007 ---------------- Wed Jun 18 10:05:06 EDT 2025 20231006_da047 007 Update not needed Wed Jun 18 10:05:06 EDT 2025 mktemplate-sess completed 20231006_da047 Registration ----------------------------- register-sess -s 20231006_da047 -d /Volumes/umms-hillmera/asem_ptsd/DA047 -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg -------------------------------------------------------------- register-sess logfile is /Volumes/umms-hillmera/asem_ptsd/DA047/log/register-sess.20231006_da047.log -------------------------------------------------------------- Wed Jun 18 10:05:06 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047 /Applications/freesurfer/fsfast/bin/register-sess -s 20231006_da047 -d /Volumes/umms-hillmera/asem_ptsd/DA047 -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 Session: /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 ---------------- Wed Jun 18 10:05:06 EDT 2025 -------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 bbregister --s 20231006_da047 --init-coreg --6 --bold --mov bold/template.nii.gz --reg bold/register.dof6.dat --lta bold/register.dof6.lta --init-reg-out bold/init.register.dof6.dat tmp bold/tmp.bbregister.75241 Log file is bold/register.dof6.log Wed Jun 18 10:05:07 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 /Applications/freesurfer/bin/bbregister --s 20231006_da047 --init-coreg --6 --bold --mov bold/template.nii.gz --reg bold/register.dof6.dat --lta bold/register.dof6.lta --init-reg-out bold/init.register.dof6.dat FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 FREESURFER_HOME /Applications/freesurfer mri_convert bold/template.nii.gz bold/tmp.bbregister.75241/template.nii mri_convert bold/template.nii.gz bold/tmp.bbregister.75241/template.nii reading from bold/template.nii.gz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to bold/tmp.bbregister.75241/template.nii... mri_coreg --s 20231006_da047 --mov bold/tmp.bbregister.75241/template.nii --regdat bold/tmp.bbregister.75241/reg.init.dat --reg bold/tmp.bbregister.75241/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 cmdline mri_coreg --s 20231006_da047 --mov bold/tmp.bbregister.75241/template.nii --regdat bold/tmp.bbregister.75241/reg.init.dat --reg bold/tmp.bbregister.75241/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov bold/tmp.bbregister.75241/template.nii Reading in ref /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/brainmask.mgz Reading in and applying refmask /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz Setting cras translation parameters to align volume centers Init matrix params -3.4393 27.7851 -14.6767 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 3.43932; 0.00000 1.00000 0.00000 -27.78510; 0.00000 0.00000 1.00000 14.67671; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt -3.4393 27.7851 -14.6767 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 1087.0000 mov gstd 1.8914 1.8914 1.8914 Smoothing mov refsat = 115.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0385559345 nhits = 179166 out of 16777216, Percent Overlap: 68.3 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -3.43932; 0.00000 1.00000 0.00000 27.78510; 0.00000 0.00000 1.00000 -14.67671; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.00000 0.00000 -1.00000 255.00000; 0.00000 1.00000 0.00000 0.00000; -1.00000 0.00000 0.00000 215.00000; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -3.43932 27.78510 -14.67671 0.00000 0.00000 0.00000 -1.0335202 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: -3.439316 27.785095 -14.676712 0.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0385559797 #@# 4 188 -3.43932 27.78510 -14.67671 0.00000 0.00000 0.00000 -1.0385560 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.038556 #@# 4 195 -3.51136 27.78510 -14.67671 0.00000 0.00000 0.00000 -1.0385648 #@# 4 204 -3.51136 27.65890 -14.67671 0.00000 0.00000 0.00000 -1.0385932 #@# 4 205 -3.51136 27.62304 -14.67671 0.00000 0.00000 0.00000 -1.0385944 #@# 4 209 -3.51136 27.63304 -13.67671 0.00000 0.00000 0.00000 -1.0391053 #@# 4 213 -3.51136 27.63304 -14.05868 0.00000 0.00000 0.00000 -1.0392648 #@# 4 214 -3.51136 27.63304 -14.02737 0.00000 0.00000 0.00000 -1.0392692 #@# 4 215 -3.51136 27.63304 -13.99879 0.00000 0.00000 0.00000 -1.0392706 #@# 4 225 -3.51136 27.63304 -13.99879 -0.02200 0.00000 0.00000 -1.0392711 #@# 4 226 -3.51136 27.63304 -13.99879 -0.01200 0.00000 0.00000 -1.0392712 #@# 4 241 -3.51136 27.63304 -13.99879 -0.01200 0.00000 -0.01000 -1.0392714 powell nthiter 1: fret = -1.039271 #@# 4 250 -3.52168 27.63304 -13.99879 -0.01200 0.00000 -0.01000 -1.0392715 #@# 4 259 -3.52168 27.65115 -13.99879 -0.01200 0.00000 -0.01000 -1.0392724 #@# 4 277 -3.52168 27.66115 -13.99879 -0.03134 0.00000 -0.01000 -1.0392725 Powell done niters total = 1 OptTimeSec 4.9 sec OptTimeMin 0.08 min nEvals 294 Final optimized parameters -3.52167869 27.66115379 -13.99879265 -0.03133912 0.00000000 -0.01000000 Final matrix parameters -3.5217 27.6612 -13.9988 -0.0313 0.0000 -0.0218 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.039272583265022 --------------------------------- Final RefRAS-to-MovRAS 1.00000 -0.00017 0.00000 -3.52168; 0.00017 1.00000 -0.00055 27.66115; 0.00000 0.00055 1.00000 -13.99879; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.00017 -0.00055 -1.00000 255.17159; 0.00000 1.00000 -0.00055 -0.60789; -1.00000 0.00000 -0.00017 214.93999; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters -3.5217 27.6612 -13.9988 -0.0313 0.0000 -0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters -3.5217 27.6612 -13.9988 -0.0313 0.0000 -0.0100 nhits = 178612 out of 16777216, Percent Overlap: 68.1 mri_coreg RunTimeSec 36.3 sec To check run: tkregisterfv --mov bold/tmp.bbregister.75241/template.nii --targ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/brainmask.mgz --reg bold/tmp.bbregister.75241/mri_coreg.lta --s 20231006_da047 --surfs mri_coreg done mri_segreg --mov bold/tmp.bbregister.75241/template.nii --init-reg bold/tmp.bbregister.75241/reg.init.dat --out-reg bold/tmp.bbregister.75241/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 mri_segreg --mov bold/tmp.bbregister.75241/template.nii --init-reg bold/tmp.bbregister.75241/reg.init.dat --out-reg bold/tmp.bbregister.75241/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/tmp.bbregister.75241/template.nii regfile bold/tmp.bbregister.75241/reg.init.dat subject 20231006_da047 dof 6 outregfile bold/tmp.bbregister.75241/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750646160 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.00017 1.00000 -0.00055 0.87605; 1.00000 -0.00017 0.00000 -1.08237; 0.00000 0.00055 1.00000 0.67792; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.988632 1 -25.0 -25.0 25.0 1.037071 2 -25.0 25.0 -25.0 1.056016 3 -25.0 25.0 25.0 1.025410 4 25.0 -25.0 -25.0 1.075703 5 25.0 -25.0 25.0 1.016784 6 25.0 25.0 -25.0 1.003132 7 25.0 25.0 25.0 1.006988 REL: 8 1.978342 8.209736 1.026217 rel = 1.9278 Initial costs ---------------- Number of surface hits 2399 WM Intensity 376.9654 +/- 59.9322 Ctx Intensity 258.3254 +/- 39.6541 Pct Contrast -36.9666 +/- 14.7759 Cost 1.9783 RelCost 1.9278 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0904 1.0904 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0747 1.0747 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0698 1.0698 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 1.0616 1.0616 0.0 13 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.0000 1.0552 1.0552 0.0 22 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.0000 1.0477 1.0477 0.0 46 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.0000 1.0467 1.0467 0.0 51 -4.0000 -4.0000 0.0000 4.0000 4.0000 -4.0000 1.0337 1.0337 0.0 52 -4.0000 -4.0000 0.0000 4.0000 4.0000 0.0000 1.0149 1.0149 0.0 319 0.0000 -4.0000 4.0000 4.0000 0.0000 0.0000 1.0094 1.0094 0.0 467 0.0000 4.0000 4.0000 -4.0000 4.0000 4.0000 0.9925 0.9925 0.0 Brute Force -------------------------- Min cost was 0.992500 Number of iterations 729 Search time 0.650132 sec Parameters at best (transmm, rotdeg) 0.000 4.000 4.000 -4.000 4.000 4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 4 2 4 3 -4 4 4 5 4 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.992500 9 -0.109 4.000 4.000 -4.000 4.000 4.000 0.9919017513 10 -0.111 4.000 4.000 -4.000 4.000 4.000 0.9918546002 11 -0.178 4.000 4.000 -4.000 4.000 4.000 0.9910447834 13 -0.152 4.000 4.000 -4.000 4.000 4.000 0.9908412440 14 -0.157 4.000 4.000 -4.000 4.000 4.000 0.9908402935 15 -0.155 4.000 4.000 -4.000 4.000 4.000 0.9908394162 18 -0.155 5.000 4.000 -4.000 4.000 4.000 0.9857779024 22 -0.155 4.618 4.000 -4.000 4.000 4.000 0.9767029396 25 -0.155 4.526 4.000 -4.000 4.000 4.000 0.9757312006 27 -0.155 4.562 4.000 -4.000 4.000 4.000 0.9749475651 28 -0.155 4.563 4.000 -4.000 4.000 4.000 0.9749431629 29 -0.155 4.568 4.000 -4.000 4.000 4.000 0.9749312757 31 -0.155 4.570 4.000 -4.000 4.000 4.000 0.9749296062 32 -0.155 4.571 4.000 -4.000 4.000 4.000 0.9749295051 39 -0.155 4.571 4.382 -4.000 4.000 4.000 0.9740548032 40 -0.155 4.571 4.244 -4.000 4.000 4.000 0.9721696673 42 -0.155 4.571 4.245 -4.000 4.000 4.000 0.9721241433 45 -0.155 4.571 4.258 -4.000 4.000 4.000 0.9719854965 46 -0.155 4.571 4.257 -4.000 4.000 4.000 0.9719775719 47 -0.155 4.571 4.255 -4.000 4.000 4.000 0.9719688205 49 -0.155 4.571 4.254 -4.000 4.000 4.000 0.9719677427 60 -0.155 4.571 4.254 -4.038 4.000 4.000 0.9716393401 62 -0.155 4.571 4.254 -4.027 4.000 4.000 0.9716112291 63 -0.155 4.571 4.254 -4.030 4.000 4.000 0.9716100456 79 -0.155 4.571 4.254 -4.029 3.996 4.000 0.9715593941 89 -0.155 4.571 4.254 -4.029 3.996 4.061 0.9697502533 91 -0.155 4.571 4.254 -4.029 3.996 4.086 0.9697182697 92 -0.155 4.571 4.254 -4.029 3.996 4.077 0.9696844675 93 -0.155 4.571 4.254 -4.029 3.996 4.075 0.9696836360 94 -0.155 4.571 4.254 -4.029 3.996 4.074 0.9696829440 96 -0.155 4.571 4.254 -4.029 3.996 4.072 0.9696825986 109 -0.163 4.600 4.267 -4.030 3.996 4.076 0.9695581807 110 -0.161 4.594 4.264 -4.030 3.996 4.075 0.9694071081 111 -0.159 4.587 4.261 -4.029 3.996 4.075 0.9693437399 113 -0.159 4.588 4.261 -4.029 3.996 4.075 0.9693435166 powell nthiter 1: fret = 0.969344 124 -0.250 4.588 4.261 -4.029 3.996 4.075 0.9692658135 125 -0.215 4.588 4.261 -4.029 3.996 4.075 0.9689027823 127 -0.218 4.588 4.261 -4.029 3.996 4.075 0.9688898259 129 -0.224 4.588 4.261 -4.029 3.996 4.075 0.9688754243 130 -0.225 4.588 4.261 -4.029 3.996 4.075 0.9688738313 139 -0.225 4.588 4.261 -4.029 3.996 4.121 0.9687203372 141 -0.225 4.588 4.261 -4.029 3.996 4.102 0.9685680345 144 -0.225 4.588 4.261 -4.029 3.996 4.098 0.9685609027 157 -0.225 4.588 4.267 -4.029 3.996 4.098 0.9685039131 168 -0.225 4.588 4.267 -3.978 3.996 4.098 0.9681744099 170 -0.225 4.588 4.267 -3.991 3.996 4.098 0.9681304127 173 -0.225 4.588 4.267 -3.993 3.996 4.098 0.9681289363 174 -0.225 4.588 4.267 -3.994 3.996 4.098 0.9681284256 183 -0.225 4.588 4.267 -3.994 3.998 4.098 0.9681206546 185 -0.225 4.588 4.267 -3.994 4.000 4.098 0.9681192705 187 -0.225 4.588 4.267 -3.994 3.999 4.098 0.9681192503 198 -0.227 4.595 4.270 -3.994 3.999 4.099 0.9680433383 199 -0.228 4.602 4.273 -3.994 3.999 4.100 0.9680173773 200 -0.229 4.603 4.273 -3.994 3.999 4.100 0.9680164700 202 -0.303 4.635 4.293 -3.960 4.003 4.128 0.9669166709 205 -0.422 4.687 4.324 -3.905 4.009 4.173 0.9652168829 208 -1.188 5.020 4.524 -3.550 4.045 4.463 0.9604971574 214 -1.165 5.010 4.519 -3.561 4.044 4.454 0.9601819164 217 -1.174 5.014 4.521 -3.557 4.045 4.457 0.9601223357 219 -1.173 5.013 4.521 -3.557 4.044 4.457 0.9601221557 220 -1.173 5.013 4.521 -3.557 4.045 4.457 0.9601215639 powell nthiter 2: fret = 0.960122 229 -1.186 5.061 4.542 -3.560 4.044 4.463 0.9596707093 231 -1.182 5.048 4.536 -3.559 4.044 4.461 0.9593595685 234 -1.181 5.043 4.534 -3.559 4.044 4.461 0.9592977004 236 -1.181 5.044 4.534 -3.559 4.044 4.461 0.9592950239 249 -1.181 5.044 4.534 -3.559 4.044 4.462 0.9592905714 257 -1.181 5.044 4.654 -3.559 4.044 4.462 0.9583322846 259 -1.181 5.044 4.606 -3.559 4.044 4.462 0.9573273610 271 -1.181 5.044 4.606 -3.584 4.044 4.462 0.9572560851 273 -1.181 5.044 4.606 -3.577 4.044 4.462 0.9572223665 274 -1.181 5.044 4.606 -3.575 4.044 4.462 0.9572211341 275 -1.181 5.044 4.606 -3.574 4.044 4.462 0.9572210279 287 -1.181 5.044 4.606 -3.574 4.058 4.462 0.9570461174 288 -1.181 5.044 4.606 -3.574 4.059 4.462 0.9570447785 289 -1.181 5.044 4.606 -3.574 4.060 4.462 0.9570433809 297 -1.136 5.024 4.594 -3.595 4.059 4.445 0.9570081478 299 -1.158 5.034 4.600 -3.585 4.060 4.453 0.9560828364 powell nthiter 3: fret = 0.956083 311 -1.159 5.037 4.602 -3.585 4.060 4.454 0.9560765216 313 -1.158 5.036 4.601 -3.585 4.060 4.454 0.9560727747 324 -1.158 5.036 4.601 -3.585 4.060 4.453 0.9560185262 326 -1.158 5.036 4.601 -3.585 4.060 4.445 0.9557448693 339 -1.158 5.036 4.588 -3.585 4.060 4.445 0.9557194726 340 -1.158 5.036 4.593 -3.585 4.060 4.445 0.9556861697 341 -1.158 5.036 4.594 -3.585 4.060 4.445 0.9556844974 352 -1.158 5.036 4.594 -3.590 4.060 4.445 0.9556833384 353 -1.158 5.036 4.594 -3.588 4.060 4.445 0.9556772174 367 -1.158 5.036 4.594 -3.588 4.057 4.445 0.9556594997 376 -1.159 5.036 4.594 -3.587 4.057 4.446 0.9556474723 377 -1.163 5.038 4.595 -3.585 4.057 4.447 0.9556326796 379 -1.162 5.037 4.595 -3.586 4.057 4.447 0.9556288719 383 -1.162 5.037 4.595 -3.586 4.057 4.447 0.9556285044 385 -1.166 5.041 4.590 -3.587 4.055 4.440 0.9556113107 391 -1.164 5.040 4.592 -3.587 4.056 4.442 0.9555437646 393 -1.164 5.039 4.592 -3.587 4.056 4.443 0.9555398699 394 -1.164 5.039 4.592 -3.587 4.056 4.443 0.9555397120 398 -1.164 5.039 4.592 -3.587 4.056 4.443 0.9555391950 401 -1.164 5.039 4.592 -3.587 4.056 4.443 0.9555389362 powell nthiter 4: fret = 0.955539 411 -1.164 5.041 4.593 -3.587 4.056 4.443 0.9555365843 413 -1.164 5.040 4.593 -3.587 4.056 4.443 0.9555347912 421 -1.164 5.040 4.593 -3.587 4.056 4.443 0.9555334851 436 -1.164 5.040 4.600 -3.587 4.056 4.443 0.9555225681 438 -1.164 5.040 4.597 -3.587 4.056 4.443 0.9555098509 447 -1.164 5.040 4.597 -3.627 4.056 4.443 0.9553801828 448 -1.164 5.040 4.597 -3.634 4.056 4.443 0.9552991189 453 -1.164 5.040 4.597 -3.637 4.056 4.443 0.9552944959 454 -1.164 5.040 4.597 -3.636 4.056 4.443 0.9552942044 465 -1.164 5.040 4.597 -3.636 4.077 4.443 0.9551265390 466 -1.164 5.040 4.597 -3.636 4.075 4.443 0.9551208405 467 -1.164 5.040 4.597 -3.636 4.074 4.443 0.9551199561 475 -1.164 5.041 4.596 -3.636 4.074 4.442 0.9551140520 480 -1.164 5.041 4.596 -3.636 4.074 4.442 0.9551140290 481 -1.164 5.041 4.596 -3.636 4.074 4.442 0.9551140184 482 -1.166 5.044 4.598 -3.686 4.090 4.438 0.9547692832 489 -1.167 5.044 4.598 -3.691 4.091 4.437 0.9547538150 490 -1.167 5.044 4.598 -3.694 4.092 4.437 0.9547487017 492 -1.167 5.045 4.598 -3.695 4.093 4.437 0.9547462173 494 -1.167 5.045 4.598 -3.696 4.093 4.437 0.9547457403 496 -1.167 5.045 4.598 -3.697 4.093 4.437 0.9547447864 powell nthiter 5: fret = 0.954745 509 -1.168 5.049 4.600 -3.697 4.093 4.438 0.9547119382 521 -1.168 5.049 4.600 -3.697 4.093 4.437 0.9547118551 523 -1.167 5.049 4.600 -3.697 4.093 4.437 0.9547118523 524 -1.167 5.049 4.600 -3.697 4.093 4.437 0.9547117893 525 -1.168 5.049 4.600 -3.697 4.093 4.437 0.9547116603 533 -1.168 5.049 4.607 -3.697 4.093 4.437 0.9546657971 544 -1.166 5.048 4.608 -3.697 4.094 4.439 0.9546341493 563 -1.166 5.048 4.608 -3.697 4.088 4.439 0.9546164371 564 -1.166 5.048 4.608 -3.697 4.089 4.439 0.9546159952 570 -1.165 5.046 4.608 -3.666 4.079 4.442 0.9546025621 572 -1.165 5.047 4.608 -3.677 4.083 4.441 0.9545717115 573 -1.166 5.047 4.608 -3.680 4.084 4.441 0.9545716538 574 -1.166 5.047 4.608 -3.679 4.083 4.441 0.9545714184 575 -1.166 5.047 4.608 -3.679 4.083 4.441 0.9545711396 powell nthiter 6: fret = 0.954571 589 -1.167 5.051 4.610 -3.679 4.083 4.441 0.9545543833 590 -1.166 5.050 4.609 -3.679 4.083 4.441 0.9545519901 600 -1.164 5.049 4.609 -3.680 4.083 4.440 0.9545507017 601 -1.165 5.050 4.609 -3.680 4.083 4.441 0.9545487051 602 -1.165 5.050 4.609 -3.680 4.083 4.441 0.9545482468 615 -1.165 5.050 4.612 -3.680 4.083 4.441 0.9545409111 624 -1.164 5.049 4.612 -3.679 4.084 4.442 0.9545312226 625 -1.164 5.049 4.613 -3.679 4.084 4.442 0.9545305942 642 -1.164 5.049 4.613 -3.679 4.074 4.442 0.9544799959 643 -1.164 5.049 4.613 -3.679 4.075 4.442 0.9544771611 644 -1.164 5.049 4.613 -3.679 4.076 4.442 0.9544767627 651 -1.163 5.047 4.612 -3.648 4.066 4.444 0.9543774804 655 -1.163 5.047 4.612 -3.652 4.067 4.444 0.9543766863 656 -1.163 5.047 4.612 -3.651 4.067 4.444 0.9543754340 657 -1.163 5.047 4.612 -3.651 4.067 4.444 0.9543752621 659 -1.163 5.047 4.612 -3.650 4.067 4.444 0.9543750345 660 -1.163 5.047 4.612 -3.650 4.067 4.444 0.9543748067 powell nthiter 7: fret = 0.954375 673 -1.165 5.055 4.615 -3.651 4.067 4.445 0.9542740295 675 -1.165 5.056 4.616 -3.651 4.067 4.445 0.9542732800 686 -1.166 5.056 4.616 -3.650 4.067 4.446 0.9542709132 687 -1.167 5.057 4.616 -3.650 4.067 4.446 0.9542699279 688 -1.167 5.057 4.616 -3.650 4.067 4.446 0.9542699007 691 -1.167 5.057 4.616 -3.650 4.067 4.446 0.9542693140 703 -1.167 5.057 4.623 -3.650 4.067 4.446 0.9541692431 704 -1.167 5.057 4.624 -3.650 4.067 4.446 0.9541678712 712 -1.166 5.056 4.626 -3.649 4.067 4.448 0.9541398106 730 -1.166 5.056 4.626 -3.649 4.049 4.448 0.9537477756 731 -1.166 5.056 4.626 -3.649 4.048 4.448 0.9537394269 732 -1.166 5.056 4.626 -3.649 4.042 4.448 0.9537304409 734 -1.166 5.056 4.626 -3.649 4.044 4.448 0.9537256640 743 -1.166 5.055 4.626 -3.647 4.044 4.448 0.9537228359 744 -1.166 5.055 4.626 -3.648 4.044 4.448 0.9537216384 747 -1.166 5.055 4.626 -3.648 4.044 4.448 0.9537215198 748 -1.166 5.055 4.626 -3.647 4.044 4.448 0.9537213702 756 -1.167 5.059 4.631 -3.646 4.035 4.450 0.9536073197 758 -1.167 5.059 4.632 -3.646 4.034 4.450 0.9536048345 powell nthiter 8: fret = 0.953605 783 -1.157 5.054 4.629 -3.651 4.034 4.446 0.9534784623 785 -1.157 5.055 4.629 -3.651 4.034 4.446 0.9534780490 797 -1.157 5.054 4.648 -3.651 4.034 4.446 0.9532292421 800 -1.157 5.054 4.642 -3.651 4.034 4.446 0.9531625312 809 -1.156 5.054 4.643 -3.651 4.034 4.447 0.9531553537 813 -1.156 5.054 4.643 -3.651 4.034 4.447 0.9531553511 814 -1.156 5.054 4.643 -3.651 4.034 4.447 0.9531553007 822 -1.156 5.053 4.642 -3.643 4.032 4.448 0.9531422311 823 -1.156 5.054 4.642 -3.646 4.032 4.447 0.9531382012 824 -1.156 5.054 4.642 -3.646 4.032 4.447 0.9531380972 825 -1.156 5.054 4.642 -3.646 4.032 4.447 0.9531379900 828 -1.156 5.054 4.642 -3.646 4.033 4.447 0.9531375044 838 -1.157 5.057 4.648 -3.645 4.024 4.449 0.9530886879 839 -1.157 5.057 4.647 -3.645 4.025 4.449 0.9530886150 840 -1.157 5.057 4.648 -3.645 4.024 4.449 0.9530884208 851 -1.154 5.057 4.656 -3.645 4.017 4.449 0.9530572339 852 -1.155 5.057 4.654 -3.645 4.018 4.449 0.9530566398 853 -1.154 5.057 4.655 -3.645 4.018 4.449 0.9530558395 854 -1.154 5.057 4.655 -3.645 4.018 4.449 0.9530556198 powell nthiter 9: fret = 0.953056 868 -1.153 5.053 4.653 -3.644 4.018 4.448 0.9529978060 869 -1.153 5.051 4.652 -3.644 4.018 4.448 0.9529869992 870 -1.153 5.050 4.652 -3.644 4.018 4.448 0.9529855753 871 -1.152 5.050 4.651 -3.644 4.018 4.448 0.9529855051 879 -1.146 5.047 4.650 -3.647 4.017 4.445 0.9529095564 880 -1.142 5.045 4.649 -3.649 4.017 4.444 0.9529008922 881 -1.142 5.045 4.649 -3.649 4.017 4.444 0.9529006982 891 -1.143 5.047 4.651 -3.648 4.013 4.445 0.9528849717 895 -1.143 5.047 4.651 -3.649 4.014 4.445 0.9528849098 896 -1.143 5.047 4.651 -3.648 4.014 4.445 0.9528848701 905 -1.144 5.047 4.650 -3.649 4.013 4.443 0.9528714411 909 -1.144 5.047 4.650 -3.649 4.013 4.444 0.9528707935 926 -1.135 5.048 4.672 -3.647 3.994 4.444 0.9527306093 931 -1.136 5.048 4.668 -3.647 3.997 4.444 0.9527163203 936 -1.136 5.048 4.668 -3.647 3.997 4.444 0.9527159950 powell nthiter 10: fret = 0.952716 957 -1.136 5.048 4.668 -3.647 3.997 4.444 0.9527143887 959 -1.136 5.048 4.668 -3.647 3.997 4.444 0.9527141548 961 -1.136 5.048 4.668 -3.647 3.997 4.444 0.9527141333 969 -1.135 5.046 4.664 -3.648 4.003 4.443 0.9526914177 973 -1.135 5.046 4.664 -3.648 4.003 4.443 0.9526909808 983 -1.136 5.046 4.664 -3.648 4.002 4.442 0.9526839997 984 -1.136 5.046 4.664 -3.648 4.002 4.442 0.9526834576 999 -1.136 5.046 4.664 -3.647 4.002 4.442 0.9526831152 1000 -1.136 5.046 4.664 -3.647 4.002 4.442 0.9526830807 1003 -1.136 5.046 4.664 -3.647 4.002 4.442 0.9526829216 1013 -1.135 5.046 4.665 -3.647 4.000 4.442 0.9526823575 1015 -1.135 5.046 4.665 -3.647 4.001 4.442 0.9526819899 1016 -1.135 5.046 4.665 -3.647 4.001 4.442 0.9526816840 1017 -1.135 5.046 4.665 -3.647 4.001 4.442 0.9526815133 1021 -1.135 5.046 4.665 -3.647 4.001 4.442 0.9526810144 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 1.028284 1 -25.0 -25.0 25.0 0.959380 2 -25.0 25.0 -25.0 1.049960 3 -25.0 25.0 25.0 1.047398 4 25.0 -25.0 -25.0 1.010401 5 25.0 -25.0 25.0 1.037027 6 25.0 25.0 -25.0 1.037559 7 25.0 25.0 25.0 1.021974 REL: 8 0.952681 8.191983 1.023998 rel = 0.930354 Number of iterations 10 Min cost was 0.952681 Number of FunctionCalls 1023 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.905939 sec Parameters at optimum (transmm) -1.13504 5.04641 4.66491 Parameters at optimum (rotdeg) -3.64696 4.00087 4.44188 Final costs ---------------- Number of surface hits 2399 WM Intensity 269.8859 +/- 114.6629 Ctx Intensity 273.1306 +/- 112.2062 Pct Contrast 2.0605 +/- 45.8248 Cost 0.9527 RelCost 1.9278 Reg at min cost was -0.08154 0.99462 0.06395 -0.13158; 0.99465 0.07712 0.06877 4.08419; -0.06347 -0.06922 0.99558 5.34736; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/tmp.bbregister.75241/bbr.pass1.dat, type = 14 Original Reg 0.00017 1.00000 -0.00055 0.87605; 1.00000 -0.00017 0.00000 -1.08237; 0.00000 0.00055 1.00000 0.67792; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.08172 0.00538 -0.06450 1.00763; 0.00535 -0.07730 -0.06877 -5.16655; 0.06347 0.06976 0.00442 -4.66945; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 10.518535 Computing change in rh position Surface-RMS-Diff-mm 9.434062 1.808268 13.558367 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov bold/tmp.bbregister.75241/template.nii --init-reg bold/tmp.bbregister.75241/bbr.pass1.dat --out-reg bold/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/tmp.bbregister.75241/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 mri_segreg --mov bold/tmp.bbregister.75241/template.nii --init-reg bold/tmp.bbregister.75241/bbr.pass1.dat --out-reg bold/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/tmp.bbregister.75241/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/tmp.bbregister.75241/template.nii regfile bold/tmp.bbregister.75241/bbr.pass1.dat subject 20231006_da047 dof 6 outregfile bold/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750579877 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.08154 0.99462 0.06395 -0.13158; 0.99465 0.07712 0.06877 4.08419; -0.06347 -0.06922 0.99558 5.34736; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.038656 1 -25.0 -25.0 25.0 1.012203 2 -25.0 25.0 -25.0 1.041423 3 -25.0 25.0 25.0 1.029611 4 25.0 -25.0 -25.0 1.036571 5 25.0 -25.0 25.0 1.032276 6 25.0 25.0 -25.0 1.013314 7 25.0 25.0 25.0 1.041020 REL: 8 1.024508 8.245075 1.030634 rel = 0.994055 Initial costs ---------------- Number of surface hits 239836 WM Intensity 271.5859 +/- 114.7456 Ctx Intensity 269.2880 +/- 112.9365 Pct Contrast -0.6085 +/- 46.3535 Cost 1.0245 RelCost 0.9941 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.9598 0.9598 0.0 15 -0.1000 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.9588 0.9588 0.0 33 -0.1000 -0.1000 0.0000 -0.1000 0.1000 -0.1000 0.9574 0.9574 0.0 54 -0.1000 -0.1000 0.1000 -0.1000 -0.1000 -0.1000 0.9558 0.9558 0.0 81 -0.1000 0.0000 -0.1000 -0.1000 -0.1000 -0.1000 0.9545 0.9545 0.0 162 -0.1000 0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.9533 0.9533 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.9527 0.9527 0.0 Brute Force -------------------------- Min cost was 0.952681 Number of iterations 729 Search time 0.627749 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 1.024508 2 1.000 0.000 0.000 0.000 0.000 0.000 1.0228885238 6 0.618 0.000 0.000 0.000 0.000 0.000 1.0217679653 8 0.683 0.000 0.000 0.000 0.000 0.000 1.0217000292 10 0.657 0.000 0.000 0.000 0.000 0.000 1.0216517622 11 0.658 0.000 0.000 0.000 0.000 0.000 1.0216505311 12 0.662 0.000 0.000 0.000 0.000 0.000 1.0216473410 14 0.663 0.000 0.000 0.000 0.000 0.000 1.0216468253 15 0.664 0.000 0.000 0.000 0.000 0.000 1.0216467114 25 0.664 0.003 0.000 0.000 0.000 0.000 1.0216413789 27 0.664 0.005 0.000 0.000 0.000 0.000 1.0216411303 31 0.664 0.005 -1.618 0.000 0.000 0.000 1.0097935726 36 0.664 0.005 -1.520 0.000 0.000 0.000 1.0095926500 43 0.664 0.005 -1.521 1.000 0.000 0.000 1.0028188325 46 0.664 0.005 -1.521 1.618 0.000 0.000 1.0026393027 48 0.664 0.005 -1.521 1.331 0.000 0.000 1.0017245706 51 0.664 0.005 -1.521 1.359 0.000 0.000 1.0016747170 53 0.664 0.005 -1.521 1.353 0.000 0.000 1.0016717109 55 0.664 0.005 -1.521 1.352 0.000 0.000 1.0016716703 62 0.664 0.005 -1.521 1.352 -0.618 0.000 0.9984721499 64 0.664 0.005 -1.521 1.352 -0.547 0.000 0.9984051751 66 0.664 0.005 -1.521 1.352 -0.575 0.000 0.9983913653 81 0.664 0.005 -1.521 1.352 -0.576 0.057 0.9981955630 86 0.664 0.005 -1.521 1.352 -0.576 0.056 0.9981950730 powell nthiter 1: fret = 0.998195 97 0.670 0.005 -1.521 1.352 -0.576 0.056 0.9981881897 99 0.681 0.005 -1.521 1.352 -0.576 0.056 0.9981789457 100 0.684 0.005 -1.521 1.352 -0.576 0.056 0.9981786007 102 0.683 0.005 -1.521 1.352 -0.576 0.056 0.9981785152 108 0.683 0.387 -1.521 1.352 -0.576 0.056 0.9961900282 113 0.683 0.389 -1.521 1.352 -0.576 0.056 0.9961861415 114 0.683 0.392 -1.521 1.352 -0.576 0.056 0.9961844016 123 0.683 0.392 -1.674 1.352 -0.576 0.056 0.9961052824 124 0.683 0.392 -1.634 1.352 -0.576 0.056 0.9959583349 125 0.683 0.392 -1.605 1.352 -0.576 0.056 0.9958622895 127 0.683 0.392 -1.601 1.352 -0.576 0.056 0.9958616634 128 0.683 0.392 -1.602 1.352 -0.576 0.056 0.9958615920 135 0.683 0.392 -1.602 1.734 -0.576 0.056 0.9951596033 136 0.683 0.392 -1.602 1.696 -0.576 0.056 0.9951220371 138 0.683 0.392 -1.602 1.694 -0.576 0.056 0.9951184239 139 0.683 0.392 -1.602 1.682 -0.576 0.056 0.9951067601 141 0.683 0.392 -1.602 1.680 -0.576 0.056 0.9951063879 142 0.683 0.392 -1.602 1.679 -0.576 0.056 0.9951062524 154 0.683 0.392 -1.602 1.678 -0.605 0.056 0.9950986835 156 0.683 0.392 -1.602 1.678 -0.593 0.056 0.9950811531 157 0.683 0.392 -1.602 1.678 -0.592 0.056 0.9950798007 158 0.683 0.392 -1.602 1.678 -0.586 0.056 0.9950787136 159 0.683 0.392 -1.602 1.678 -0.588 0.056 0.9950775614 169 0.683 0.392 -1.602 1.678 -0.588 0.059 0.9950687340 170 0.683 0.392 -1.602 1.678 -0.588 0.091 0.9950606797 176 0.683 0.392 -1.602 1.678 -0.588 0.089 0.9950604613 177 0.683 0.392 -1.602 1.678 -0.588 0.090 0.9950604144 178 0.702 0.778 -1.684 2.004 -0.600 0.125 0.9935839821 183 0.713 1.017 -1.735 2.206 -0.608 0.146 0.9931376917 186 0.715 1.052 -1.742 2.235 -0.609 0.150 0.9931020170 188 0.714 1.045 -1.740 2.229 -0.609 0.149 0.9930975675 193 0.714 1.044 -1.740 2.229 -0.609 0.149 0.9930974810 powell nthiter 2: fret = 0.993097 199 1.096 1.044 -1.740 2.229 -0.609 0.149 0.9925515775 200 1.095 1.044 -1.740 2.229 -0.609 0.149 0.9925475750 201 0.956 1.044 -1.740 2.229 -0.609 0.149 0.9924011907 208 0.957 1.044 -1.740 2.229 -0.609 0.149 0.9924006697 215 0.957 1.044 -1.740 2.229 -0.609 0.531 0.9919225995 216 0.957 1.044 -1.740 2.229 -0.609 0.418 0.9915026768 217 0.957 1.044 -1.740 2.229 -0.609 0.374 0.9913346354 218 0.957 1.044 -1.740 2.229 -0.609 0.288 0.9913282496 219 0.957 1.044 -1.740 2.229 -0.609 0.330 0.9912800282 221 0.957 1.044 -1.740 2.229 -0.609 0.346 0.9912688222 223 0.957 1.044 -1.740 2.229 -0.609 0.340 0.9912671592 224 0.957 1.044 -1.740 2.229 -0.609 0.342 0.9912662395 225 0.957 1.044 -1.740 2.229 -0.609 0.343 0.9912661309 231 0.957 1.044 -2.358 2.229 -0.609 0.343 0.9901722544 233 0.957 1.044 -2.125 2.229 -0.609 0.343 0.9889410862 236 0.957 1.044 -2.133 2.229 -0.609 0.343 0.9889236771 237 0.957 1.044 -2.137 2.229 -0.609 0.343 0.9889199709 238 0.957 1.044 -2.139 2.229 -0.609 0.343 0.9889198819 240 0.957 1.044 -2.138 2.229 -0.609 0.343 0.9889197144 247 0.957 1.044 -2.138 2.290 -0.609 0.343 0.9889187018 255 0.957 1.044 -2.138 2.293 -0.609 0.343 0.9889186489 256 0.957 1.044 -2.138 2.292 -0.609 0.343 0.9889185633 266 0.957 1.044 -2.138 2.292 -0.602 0.343 0.9889148816 267 0.957 1.044 -2.138 2.292 -0.604 0.343 0.9889145328 275 0.955 0.998 -2.128 2.252 -0.602 0.339 0.9887780642 276 0.954 0.971 -2.123 2.230 -0.601 0.336 0.9887457470 277 0.953 0.959 -2.120 2.220 -0.601 0.335 0.9887376603 280 0.953 0.949 -2.118 2.212 -0.601 0.334 0.9887298691 281 0.953 0.949 -2.118 2.211 -0.601 0.334 0.9887295099 283 0.953 0.947 -2.118 2.210 -0.601 0.334 0.9887292358 powell nthiter 3: fret = 0.988729 294 0.976 0.947 -2.118 2.210 -0.601 0.334 0.9887132967 295 0.995 0.947 -2.118 2.210 -0.601 0.334 0.9887028059 300 0.993 0.947 -2.118 2.210 -0.601 0.334 0.9887022880 302 0.991 0.947 -2.118 2.210 -0.601 0.334 0.9887020515 313 0.991 0.947 -2.118 2.210 -0.601 0.244 0.9886438972 314 0.991 0.947 -2.118 2.210 -0.601 0.271 0.9885599689 315 0.991 0.947 -2.118 2.210 -0.601 0.283 0.9885497451 317 0.991 0.947 -2.118 2.210 -0.601 0.280 0.9885475658 350 0.991 0.947 -2.118 2.210 -0.614 0.280 0.9885224598 351 0.991 0.947 -2.118 2.210 -0.615 0.280 0.9885222373 361 0.991 0.947 -2.118 2.210 -0.615 0.280 0.9885221319 362 0.991 0.949 -2.118 2.212 -0.615 0.280 0.9885217425 powell nthiter 4: fret = 0.988522 379 0.994 0.951 -2.118 2.213 -0.615 0.280 0.9885217424 381 0.993 0.951 -2.118 2.213 -0.615 0.280 0.9885216625 394 0.993 0.951 -2.118 2.213 -0.615 0.284 0.9885177016 405 0.993 0.951 -2.110 2.213 -0.615 0.284 0.9885085687 417 0.993 0.951 -2.110 2.212 -0.615 0.284 0.9885083718 428 0.993 0.951 -2.110 2.212 -0.619 0.284 0.9885028632 430 0.993 0.951 -2.110 2.212 -0.621 0.284 0.9885022547 441 0.993 0.953 -2.110 2.213 -0.621 0.284 0.9885013122 442 0.993 0.955 -2.111 2.215 -0.621 0.285 0.9885010084 443 0.993 0.954 -2.111 2.215 -0.621 0.284 0.9885009462 444 0.993 0.954 -2.111 2.214 -0.621 0.284 0.9885008894 446 0.995 0.957 -2.103 2.216 -0.626 0.289 0.9884854895 453 0.995 0.957 -2.102 2.216 -0.626 0.289 0.9884854510 454 0.995 0.957 -2.102 2.216 -0.626 0.289 0.9884854329 powell nthiter 5: fret = 0.988485 467 1.000 0.957 -2.102 2.216 -0.626 0.289 0.9884848650 468 0.998 0.957 -2.102 2.216 -0.626 0.289 0.9884839565 483 0.998 0.957 -2.102 2.216 -0.626 0.290 0.9884838576 494 0.998 0.958 -2.102 2.216 -0.626 0.290 0.9884837904 495 0.998 0.958 -2.102 2.217 -0.626 0.290 0.9884837245 498 0.998 0.959 -2.103 2.218 -0.626 0.290 0.9884837077 522 0.998 0.958 -2.102 2.217 -0.627 0.290 0.9884834016 530 0.998 0.958 -2.102 2.217 -0.627 0.290 0.9884833806 532 0.998 0.958 -2.103 2.217 -0.627 0.290 0.9884833547 533 0.998 0.958 -2.103 2.217 -0.627 0.290 0.9884833014 538 0.998 0.958 -2.103 2.217 -0.627 0.290 0.9884832678 powell nthiter 6: fret = 0.988483 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 1.020245 1 -25.0 -25.0 25.0 1.021641 2 -25.0 25.0 -25.0 1.024180 3 -25.0 25.0 25.0 1.013009 4 25.0 -25.0 -25.0 1.040236 5 25.0 -25.0 25.0 1.036301 6 25.0 25.0 -25.0 1.003885 7 25.0 25.0 25.0 1.021881 REL: 8 0.988483 8.181378 1.022672 rel = 0.966569 Number of iterations 6 Min cost was 0.988483 Number of FunctionCalls 616 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 28.414067 sec Parameters at optimum (transmm) 0.99783 0.95822 -2.10294 Parameters at optimum (rotdeg) 2.21701 -0.62711 0.29007 Final costs ---------------- Number of surface hits 239836 WM Intensity 274.1005 +/- 111.8385 Ctx Intensity 276.1199 +/- 112.6135 Pct Contrast 0.5310 +/- 46.5089 Cost 0.9885 RelCost 0.9941 Reg at min cost was -0.08631 0.99486 0.05288 0.78643; 0.99593 0.08478 0.03047 4.83146; -0.02583 -0.05529 0.99814 3.39665; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/register.dof6.dat, type = 14 Original Reg -0.08154 0.99462 0.06395 -0.13158; 0.99465 0.07712 0.06877 4.08419; -0.06347 -0.06922 0.99558 5.34736; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00477 -0.00025 0.01107 -0.91801; -0.00129 -0.00766 0.03830 -0.74728; -0.03763 -0.01393 -0.00256 1.95072; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 3.418695 Computing change in rh position Surface-RMS-Diff-mm 2.605381 1.117176 4.872053 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done MinCost: 0.988483 274.100526 276.119916 0.530968 tkregister2_cmdl --mov bold/template.nii.gz --reg bold/register.dof6.dat --noedit --ltaout bold/register.dof6.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/template.nii.gz reg file bold/register.dof6.dat LoadVol 0 ZeroCRAS 0 7.4.1 Diagnostic Level -1 ---- Input registration matrix -------- -0.08631 0.99486 0.05288 0.78643; 0.99593 0.08478 0.03047 4.83146; -0.02583 -0.05529 0.99814 3.39665; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/template.nii.gz Tmov: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -88.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -0.08631 0.99486 0.05288 0.78643; 0.99593 0.08478 0.03047 4.83146; -0.02583 -0.05529 0.99814 3.39665; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = 20231006_da047 RegMat --------------------------- -0.08631 0.99486 0.05288 0.78643; 0.99593 0.08478 0.03047 4.83146; -0.02583 -0.05529 0.99814 3.39665; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Wed Jun 18 10:05:07 EDT 2025 Ended at Wed Jun 18 10:06:20 EDT 2025 BBR-Run-Time-Sec 73 bbregister Done To check results, run: tkregisterfv --mov bold/template.nii.gz --reg bold/register.dof6.lta --surfs --sd /Volumes/umms-hillmera/asem_ptsd/DA047 Run: 002 ---------------- Wed Jun 18 10:06:20 EDT 2025 -------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 bbregister --s 20231006_da047 --init-coreg --6 --bold --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --lta bold/002/register.dof6.lta --init-reg-out bold/002/init.register.dof6.dat tmp bold/002/tmp.bbregister.75343 Log file is bold/002/register.dof6.log Wed Jun 18 10:06:21 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 /Applications/freesurfer/bin/bbregister --s 20231006_da047 --init-coreg --6 --bold --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --lta bold/002/register.dof6.lta --init-reg-out bold/002/init.register.dof6.dat FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 FREESURFER_HOME /Applications/freesurfer mri_convert bold/002/template.nii.gz bold/002/tmp.bbregister.75343/template.nii mri_convert bold/002/template.nii.gz bold/002/tmp.bbregister.75343/template.nii reading from bold/002/template.nii.gz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to bold/002/tmp.bbregister.75343/template.nii... mri_coreg --s 20231006_da047 --mov bold/002/tmp.bbregister.75343/template.nii --regdat bold/002/tmp.bbregister.75343/reg.init.dat --reg bold/002/tmp.bbregister.75343/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 cmdline mri_coreg --s 20231006_da047 --mov bold/002/tmp.bbregister.75343/template.nii --regdat bold/002/tmp.bbregister.75343/reg.init.dat --reg bold/002/tmp.bbregister.75343/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov bold/002/tmp.bbregister.75343/template.nii Reading in ref /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/brainmask.mgz Reading in and applying refmask /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz Setting cras translation parameters to align volume centers Init matrix params -3.4393 27.7851 -14.6767 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 3.43932; 0.00000 1.00000 0.00000 -27.78510; 0.00000 0.00000 1.00000 14.67671; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt -3.4393 27.7851 -14.6767 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 1087.0000 mov gstd 1.8914 1.8914 1.8914 Smoothing mov refsat = 115.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0385559345 nhits = 179166 out of 16777216, Percent Overlap: 68.3 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -3.43932; 0.00000 1.00000 0.00000 27.78510; 0.00000 0.00000 1.00000 -14.67671; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.00000 0.00000 -1.00000 255.00000; 0.00000 1.00000 0.00000 0.00000; -1.00000 0.00000 0.00000 215.00000; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -3.43932 27.78510 -14.67671 0.00000 0.00000 0.00000 -1.0335202 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: -3.439316 27.785095 -14.676712 0.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0385559797 #@# 4 188 -3.43932 27.78510 -14.67671 0.00000 0.00000 0.00000 -1.0385560 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.038556 #@# 4 195 -3.51136 27.78510 -14.67671 0.00000 0.00000 0.00000 -1.0385648 #@# 4 204 -3.51136 27.65890 -14.67671 0.00000 0.00000 0.00000 -1.0385932 #@# 4 205 -3.51136 27.62304 -14.67671 0.00000 0.00000 0.00000 -1.0385944 #@# 4 209 -3.51136 27.63304 -13.67671 0.00000 0.00000 0.00000 -1.0391053 #@# 4 213 -3.51136 27.63304 -14.05868 0.00000 0.00000 0.00000 -1.0392648 #@# 4 214 -3.51136 27.63304 -14.02737 0.00000 0.00000 0.00000 -1.0392692 #@# 4 215 -3.51136 27.63304 -13.99879 0.00000 0.00000 0.00000 -1.0392706 #@# 4 225 -3.51136 27.63304 -13.99879 -0.02200 0.00000 0.00000 -1.0392711 #@# 4 226 -3.51136 27.63304 -13.99879 -0.01200 0.00000 0.00000 -1.0392712 #@# 4 241 -3.51136 27.63304 -13.99879 -0.01200 0.00000 -0.01000 -1.0392714 powell nthiter 1: fret = -1.039271 #@# 4 250 -3.52168 27.63304 -13.99879 -0.01200 0.00000 -0.01000 -1.0392715 #@# 4 259 -3.52168 27.65115 -13.99879 -0.01200 0.00000 -0.01000 -1.0392724 #@# 4 277 -3.52168 27.66115 -13.99879 -0.03134 0.00000 -0.01000 -1.0392725 Powell done niters total = 1 OptTimeSec 5.0 sec OptTimeMin 0.08 min nEvals 294 Final optimized parameters -3.52167869 27.66115379 -13.99879265 -0.03133912 0.00000000 -0.01000000 Final matrix parameters -3.5217 27.6612 -13.9988 -0.0313 0.0000 -0.0218 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.039272583265022 --------------------------------- Final RefRAS-to-MovRAS 1.00000 -0.00017 0.00000 -3.52168; 0.00017 1.00000 -0.00055 27.66115; 0.00000 0.00055 1.00000 -13.99879; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.00017 -0.00055 -1.00000 255.17159; 0.00000 1.00000 -0.00055 -0.60789; -1.00000 0.00000 -0.00017 214.93999; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters -3.5217 27.6612 -13.9988 -0.0313 0.0000 -0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters -3.5217 27.6612 -13.9988 -0.0313 0.0000 -0.0100 nhits = 178612 out of 16777216, Percent Overlap: 68.1 mri_coreg RunTimeSec 36.9 sec To check run: tkregisterfv --mov bold/002/tmp.bbregister.75343/template.nii --targ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/brainmask.mgz --reg bold/002/tmp.bbregister.75343/mri_coreg.lta --s 20231006_da047 --surfs mri_coreg done mri_segreg --mov bold/002/tmp.bbregister.75343/template.nii --init-reg bold/002/tmp.bbregister.75343/reg.init.dat --out-reg bold/002/tmp.bbregister.75343/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 mri_segreg --mov bold/002/tmp.bbregister.75343/template.nii --init-reg bold/002/tmp.bbregister.75343/reg.init.dat --out-reg bold/002/tmp.bbregister.75343/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/002/tmp.bbregister.75343/template.nii regfile bold/002/tmp.bbregister.75343/reg.init.dat subject 20231006_da047 dof 6 outregfile bold/002/tmp.bbregister.75343/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1751106066 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.00017 1.00000 -0.00055 0.87605; 1.00000 -0.00017 0.00000 -1.08237; 0.00000 0.00055 1.00000 0.67792; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.988632 1 -25.0 -25.0 25.0 1.037071 2 -25.0 25.0 -25.0 1.056016 3 -25.0 25.0 25.0 1.025410 4 25.0 -25.0 -25.0 1.075703 5 25.0 -25.0 25.0 1.016784 6 25.0 25.0 -25.0 1.003132 7 25.0 25.0 25.0 1.006988 REL: 8 1.978342 8.209736 1.026217 rel = 1.9278 Initial costs ---------------- Number of surface hits 2399 WM Intensity 376.9654 +/- 59.9322 Ctx Intensity 258.3254 +/- 39.6541 Pct Contrast -36.9666 +/- 14.7759 Cost 1.9783 RelCost 1.9278 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0904 1.0904 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0747 1.0747 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0698 1.0698 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 1.0616 1.0616 0.0 13 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.0000 1.0552 1.0552 0.0 22 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.0000 1.0477 1.0477 0.0 46 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.0000 1.0467 1.0467 0.0 51 -4.0000 -4.0000 0.0000 4.0000 4.0000 -4.0000 1.0337 1.0337 0.0 52 -4.0000 -4.0000 0.0000 4.0000 4.0000 0.0000 1.0149 1.0149 0.0 319 0.0000 -4.0000 4.0000 4.0000 0.0000 0.0000 1.0094 1.0094 0.0 467 0.0000 4.0000 4.0000 -4.0000 4.0000 4.0000 0.9925 0.9925 0.0 Brute Force -------------------------- Min cost was 0.992500 Number of iterations 729 Search time 1.002761 sec Parameters at best (transmm, rotdeg) 0.000 4.000 4.000 -4.000 4.000 4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 4 2 4 3 -4 4 4 5 4 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.992500 9 -0.109 4.000 4.000 -4.000 4.000 4.000 0.9919017513 10 -0.111 4.000 4.000 -4.000 4.000 4.000 0.9918546002 11 -0.178 4.000 4.000 -4.000 4.000 4.000 0.9910447834 13 -0.152 4.000 4.000 -4.000 4.000 4.000 0.9908412440 14 -0.157 4.000 4.000 -4.000 4.000 4.000 0.9908402935 15 -0.155 4.000 4.000 -4.000 4.000 4.000 0.9908394162 18 -0.155 5.000 4.000 -4.000 4.000 4.000 0.9857779024 22 -0.155 4.618 4.000 -4.000 4.000 4.000 0.9767029396 25 -0.155 4.526 4.000 -4.000 4.000 4.000 0.9757312006 27 -0.155 4.562 4.000 -4.000 4.000 4.000 0.9749475651 28 -0.155 4.563 4.000 -4.000 4.000 4.000 0.9749431629 29 -0.155 4.568 4.000 -4.000 4.000 4.000 0.9749312757 31 -0.155 4.570 4.000 -4.000 4.000 4.000 0.9749296062 32 -0.155 4.571 4.000 -4.000 4.000 4.000 0.9749295051 39 -0.155 4.571 4.382 -4.000 4.000 4.000 0.9740548032 40 -0.155 4.571 4.244 -4.000 4.000 4.000 0.9721696673 42 -0.155 4.571 4.245 -4.000 4.000 4.000 0.9721241433 45 -0.155 4.571 4.258 -4.000 4.000 4.000 0.9719854965 46 -0.155 4.571 4.257 -4.000 4.000 4.000 0.9719775719 47 -0.155 4.571 4.255 -4.000 4.000 4.000 0.9719688205 49 -0.155 4.571 4.254 -4.000 4.000 4.000 0.9719677427 60 -0.155 4.571 4.254 -4.038 4.000 4.000 0.9716393401 62 -0.155 4.571 4.254 -4.027 4.000 4.000 0.9716112291 63 -0.155 4.571 4.254 -4.030 4.000 4.000 0.9716100456 79 -0.155 4.571 4.254 -4.029 3.996 4.000 0.9715593941 89 -0.155 4.571 4.254 -4.029 3.996 4.061 0.9697502533 91 -0.155 4.571 4.254 -4.029 3.996 4.086 0.9697182697 92 -0.155 4.571 4.254 -4.029 3.996 4.077 0.9696844675 93 -0.155 4.571 4.254 -4.029 3.996 4.075 0.9696836360 94 -0.155 4.571 4.254 -4.029 3.996 4.074 0.9696829440 96 -0.155 4.571 4.254 -4.029 3.996 4.072 0.9696825986 109 -0.163 4.600 4.267 -4.030 3.996 4.076 0.9695581807 110 -0.161 4.594 4.264 -4.030 3.996 4.075 0.9694071081 111 -0.159 4.587 4.261 -4.029 3.996 4.075 0.9693437399 113 -0.159 4.588 4.261 -4.029 3.996 4.075 0.9693435166 powell nthiter 1: fret = 0.969344 124 -0.250 4.588 4.261 -4.029 3.996 4.075 0.9692658135 125 -0.215 4.588 4.261 -4.029 3.996 4.075 0.9689027823 127 -0.218 4.588 4.261 -4.029 3.996 4.075 0.9688898259 129 -0.224 4.588 4.261 -4.029 3.996 4.075 0.9688754243 130 -0.225 4.588 4.261 -4.029 3.996 4.075 0.9688738313 139 -0.225 4.588 4.261 -4.029 3.996 4.121 0.9687203372 141 -0.225 4.588 4.261 -4.029 3.996 4.102 0.9685680345 144 -0.225 4.588 4.261 -4.029 3.996 4.098 0.9685609027 157 -0.225 4.588 4.267 -4.029 3.996 4.098 0.9685039131 168 -0.225 4.588 4.267 -3.978 3.996 4.098 0.9681744099 170 -0.225 4.588 4.267 -3.991 3.996 4.098 0.9681304127 173 -0.225 4.588 4.267 -3.993 3.996 4.098 0.9681289363 174 -0.225 4.588 4.267 -3.994 3.996 4.098 0.9681284256 183 -0.225 4.588 4.267 -3.994 3.998 4.098 0.9681206546 185 -0.225 4.588 4.267 -3.994 4.000 4.098 0.9681192705 187 -0.225 4.588 4.267 -3.994 3.999 4.098 0.9681192503 198 -0.227 4.595 4.270 -3.994 3.999 4.099 0.9680433383 199 -0.228 4.602 4.273 -3.994 3.999 4.100 0.9680173773 200 -0.229 4.603 4.273 -3.994 3.999 4.100 0.9680164700 202 -0.303 4.635 4.293 -3.960 4.003 4.128 0.9669166709 205 -0.422 4.687 4.324 -3.905 4.009 4.173 0.9652168829 208 -1.188 5.020 4.524 -3.550 4.045 4.463 0.9604971574 214 -1.165 5.010 4.519 -3.561 4.044 4.454 0.9601819164 217 -1.174 5.014 4.521 -3.557 4.045 4.457 0.9601223357 219 -1.173 5.013 4.521 -3.557 4.044 4.457 0.9601221557 220 -1.173 5.013 4.521 -3.557 4.045 4.457 0.9601215639 powell nthiter 2: fret = 0.960122 229 -1.186 5.061 4.542 -3.560 4.044 4.463 0.9596707093 231 -1.182 5.048 4.536 -3.559 4.044 4.461 0.9593595685 234 -1.181 5.043 4.534 -3.559 4.044 4.461 0.9592977004 236 -1.181 5.044 4.534 -3.559 4.044 4.461 0.9592950239 249 -1.181 5.044 4.534 -3.559 4.044 4.462 0.9592905714 257 -1.181 5.044 4.654 -3.559 4.044 4.462 0.9583322846 259 -1.181 5.044 4.606 -3.559 4.044 4.462 0.9573273610 271 -1.181 5.044 4.606 -3.584 4.044 4.462 0.9572560851 273 -1.181 5.044 4.606 -3.577 4.044 4.462 0.9572223665 274 -1.181 5.044 4.606 -3.575 4.044 4.462 0.9572211341 275 -1.181 5.044 4.606 -3.574 4.044 4.462 0.9572210279 287 -1.181 5.044 4.606 -3.574 4.058 4.462 0.9570461174 288 -1.181 5.044 4.606 -3.574 4.059 4.462 0.9570447785 289 -1.181 5.044 4.606 -3.574 4.060 4.462 0.9570433809 297 -1.136 5.024 4.594 -3.595 4.059 4.445 0.9570081478 299 -1.158 5.034 4.600 -3.585 4.060 4.453 0.9560828364 powell nthiter 3: fret = 0.956083 311 -1.159 5.037 4.602 -3.585 4.060 4.454 0.9560765216 313 -1.158 5.036 4.601 -3.585 4.060 4.454 0.9560727747 324 -1.158 5.036 4.601 -3.585 4.060 4.453 0.9560185262 326 -1.158 5.036 4.601 -3.585 4.060 4.445 0.9557448693 339 -1.158 5.036 4.588 -3.585 4.060 4.445 0.9557194726 340 -1.158 5.036 4.593 -3.585 4.060 4.445 0.9556861697 341 -1.158 5.036 4.594 -3.585 4.060 4.445 0.9556844974 352 -1.158 5.036 4.594 -3.590 4.060 4.445 0.9556833384 353 -1.158 5.036 4.594 -3.588 4.060 4.445 0.9556772174 367 -1.158 5.036 4.594 -3.588 4.057 4.445 0.9556594997 376 -1.159 5.036 4.594 -3.587 4.057 4.446 0.9556474723 377 -1.163 5.038 4.595 -3.585 4.057 4.447 0.9556326796 379 -1.162 5.037 4.595 -3.586 4.057 4.447 0.9556288719 383 -1.162 5.037 4.595 -3.586 4.057 4.447 0.9556285044 385 -1.166 5.041 4.590 -3.587 4.055 4.440 0.9556113107 391 -1.164 5.040 4.592 -3.587 4.056 4.442 0.9555437646 393 -1.164 5.039 4.592 -3.587 4.056 4.443 0.9555398699 394 -1.164 5.039 4.592 -3.587 4.056 4.443 0.9555397120 398 -1.164 5.039 4.592 -3.587 4.056 4.443 0.9555391950 401 -1.164 5.039 4.592 -3.587 4.056 4.443 0.9555389362 powell nthiter 4: fret = 0.955539 411 -1.164 5.041 4.593 -3.587 4.056 4.443 0.9555365843 413 -1.164 5.040 4.593 -3.587 4.056 4.443 0.9555347912 421 -1.164 5.040 4.593 -3.587 4.056 4.443 0.9555334851 436 -1.164 5.040 4.600 -3.587 4.056 4.443 0.9555225681 438 -1.164 5.040 4.597 -3.587 4.056 4.443 0.9555098509 447 -1.164 5.040 4.597 -3.627 4.056 4.443 0.9553801828 448 -1.164 5.040 4.597 -3.634 4.056 4.443 0.9552991189 453 -1.164 5.040 4.597 -3.637 4.056 4.443 0.9552944959 454 -1.164 5.040 4.597 -3.636 4.056 4.443 0.9552942044 465 -1.164 5.040 4.597 -3.636 4.077 4.443 0.9551265390 466 -1.164 5.040 4.597 -3.636 4.075 4.443 0.9551208405 467 -1.164 5.040 4.597 -3.636 4.074 4.443 0.9551199561 475 -1.164 5.041 4.596 -3.636 4.074 4.442 0.9551140520 480 -1.164 5.041 4.596 -3.636 4.074 4.442 0.9551140290 481 -1.164 5.041 4.596 -3.636 4.074 4.442 0.9551140184 482 -1.166 5.044 4.598 -3.686 4.090 4.438 0.9547692832 489 -1.167 5.044 4.598 -3.691 4.091 4.437 0.9547538150 490 -1.167 5.044 4.598 -3.694 4.092 4.437 0.9547487017 492 -1.167 5.045 4.598 -3.695 4.093 4.437 0.9547462173 494 -1.167 5.045 4.598 -3.696 4.093 4.437 0.9547457403 496 -1.167 5.045 4.598 -3.697 4.093 4.437 0.9547447864 powell nthiter 5: fret = 0.954745 509 -1.168 5.049 4.600 -3.697 4.093 4.438 0.9547119382 521 -1.168 5.049 4.600 -3.697 4.093 4.437 0.9547118551 523 -1.167 5.049 4.600 -3.697 4.093 4.437 0.9547118523 524 -1.167 5.049 4.600 -3.697 4.093 4.437 0.9547117893 525 -1.168 5.049 4.600 -3.697 4.093 4.437 0.9547116603 533 -1.168 5.049 4.607 -3.697 4.093 4.437 0.9546657971 544 -1.166 5.048 4.608 -3.697 4.094 4.439 0.9546341493 563 -1.166 5.048 4.608 -3.697 4.088 4.439 0.9546164371 564 -1.166 5.048 4.608 -3.697 4.089 4.439 0.9546159952 570 -1.165 5.046 4.608 -3.666 4.079 4.442 0.9546025621 572 -1.165 5.047 4.608 -3.677 4.083 4.441 0.9545717115 573 -1.166 5.047 4.608 -3.680 4.084 4.441 0.9545716538 574 -1.166 5.047 4.608 -3.679 4.083 4.441 0.9545714184 575 -1.166 5.047 4.608 -3.679 4.083 4.441 0.9545711396 powell nthiter 6: fret = 0.954571 589 -1.167 5.051 4.610 -3.679 4.083 4.441 0.9545543833 590 -1.166 5.050 4.609 -3.679 4.083 4.441 0.9545519901 600 -1.164 5.049 4.609 -3.680 4.083 4.440 0.9545507017 601 -1.165 5.050 4.609 -3.680 4.083 4.441 0.9545487051 602 -1.165 5.050 4.609 -3.680 4.083 4.441 0.9545482468 615 -1.165 5.050 4.612 -3.680 4.083 4.441 0.9545409111 624 -1.164 5.049 4.612 -3.679 4.084 4.442 0.9545312226 625 -1.164 5.049 4.613 -3.679 4.084 4.442 0.9545305942 642 -1.164 5.049 4.613 -3.679 4.074 4.442 0.9544799959 643 -1.164 5.049 4.613 -3.679 4.075 4.442 0.9544771611 644 -1.164 5.049 4.613 -3.679 4.076 4.442 0.9544767627 651 -1.163 5.047 4.612 -3.648 4.066 4.444 0.9543774804 655 -1.163 5.047 4.612 -3.652 4.067 4.444 0.9543766863 656 -1.163 5.047 4.612 -3.651 4.067 4.444 0.9543754340 657 -1.163 5.047 4.612 -3.651 4.067 4.444 0.9543752621 659 -1.163 5.047 4.612 -3.650 4.067 4.444 0.9543750345 660 -1.163 5.047 4.612 -3.650 4.067 4.444 0.9543748067 powell nthiter 7: fret = 0.954375 673 -1.165 5.055 4.615 -3.651 4.067 4.445 0.9542740295 675 -1.165 5.056 4.616 -3.651 4.067 4.445 0.9542732800 686 -1.166 5.056 4.616 -3.650 4.067 4.446 0.9542709132 687 -1.167 5.057 4.616 -3.650 4.067 4.446 0.9542699279 688 -1.167 5.057 4.616 -3.650 4.067 4.446 0.9542699007 691 -1.167 5.057 4.616 -3.650 4.067 4.446 0.9542693140 703 -1.167 5.057 4.623 -3.650 4.067 4.446 0.9541692431 704 -1.167 5.057 4.624 -3.650 4.067 4.446 0.9541678712 712 -1.166 5.056 4.626 -3.649 4.067 4.448 0.9541398106 730 -1.166 5.056 4.626 -3.649 4.049 4.448 0.9537477756 731 -1.166 5.056 4.626 -3.649 4.048 4.448 0.9537394269 732 -1.166 5.056 4.626 -3.649 4.042 4.448 0.9537304409 734 -1.166 5.056 4.626 -3.649 4.044 4.448 0.9537256640 743 -1.166 5.055 4.626 -3.647 4.044 4.448 0.9537228359 744 -1.166 5.055 4.626 -3.648 4.044 4.448 0.9537216384 747 -1.166 5.055 4.626 -3.648 4.044 4.448 0.9537215198 748 -1.166 5.055 4.626 -3.647 4.044 4.448 0.9537213702 756 -1.167 5.059 4.631 -3.646 4.035 4.450 0.9536073197 758 -1.167 5.059 4.632 -3.646 4.034 4.450 0.9536048345 powell nthiter 8: fret = 0.953605 783 -1.157 5.054 4.629 -3.651 4.034 4.446 0.9534784623 785 -1.157 5.055 4.629 -3.651 4.034 4.446 0.9534780490 797 -1.157 5.054 4.648 -3.651 4.034 4.446 0.9532292421 800 -1.157 5.054 4.642 -3.651 4.034 4.446 0.9531625312 809 -1.156 5.054 4.643 -3.651 4.034 4.447 0.9531553537 813 -1.156 5.054 4.643 -3.651 4.034 4.447 0.9531553511 814 -1.156 5.054 4.643 -3.651 4.034 4.447 0.9531553007 822 -1.156 5.053 4.642 -3.643 4.032 4.448 0.9531422311 823 -1.156 5.054 4.642 -3.646 4.032 4.447 0.9531382012 824 -1.156 5.054 4.642 -3.646 4.032 4.447 0.9531380972 825 -1.156 5.054 4.642 -3.646 4.032 4.447 0.9531379900 828 -1.156 5.054 4.642 -3.646 4.033 4.447 0.9531375044 838 -1.157 5.057 4.648 -3.645 4.024 4.449 0.9530886879 839 -1.157 5.057 4.647 -3.645 4.025 4.449 0.9530886150 840 -1.157 5.057 4.648 -3.645 4.024 4.449 0.9530884208 851 -1.154 5.057 4.656 -3.645 4.017 4.449 0.9530572339 852 -1.155 5.057 4.654 -3.645 4.018 4.449 0.9530566398 853 -1.154 5.057 4.655 -3.645 4.018 4.449 0.9530558395 854 -1.154 5.057 4.655 -3.645 4.018 4.449 0.9530556198 powell nthiter 9: fret = 0.953056 868 -1.153 5.053 4.653 -3.644 4.018 4.448 0.9529978060 869 -1.153 5.051 4.652 -3.644 4.018 4.448 0.9529869992 870 -1.153 5.050 4.652 -3.644 4.018 4.448 0.9529855753 871 -1.152 5.050 4.651 -3.644 4.018 4.448 0.9529855051 879 -1.146 5.047 4.650 -3.647 4.017 4.445 0.9529095564 880 -1.142 5.045 4.649 -3.649 4.017 4.444 0.9529008922 881 -1.142 5.045 4.649 -3.649 4.017 4.444 0.9529006982 891 -1.143 5.047 4.651 -3.648 4.013 4.445 0.9528849717 895 -1.143 5.047 4.651 -3.649 4.014 4.445 0.9528849098 896 -1.143 5.047 4.651 -3.648 4.014 4.445 0.9528848701 905 -1.144 5.047 4.650 -3.649 4.013 4.443 0.9528714411 909 -1.144 5.047 4.650 -3.649 4.013 4.444 0.9528707935 926 -1.135 5.048 4.672 -3.647 3.994 4.444 0.9527306093 931 -1.136 5.048 4.668 -3.647 3.997 4.444 0.9527163203 936 -1.136 5.048 4.668 -3.647 3.997 4.444 0.9527159950 powell nthiter 10: fret = 0.952716 957 -1.136 5.048 4.668 -3.647 3.997 4.444 0.9527143887 959 -1.136 5.048 4.668 -3.647 3.997 4.444 0.9527141548 961 -1.136 5.048 4.668 -3.647 3.997 4.444 0.9527141333 969 -1.135 5.046 4.664 -3.648 4.003 4.443 0.9526914177 973 -1.135 5.046 4.664 -3.648 4.003 4.443 0.9526909808 983 -1.136 5.046 4.664 -3.648 4.002 4.442 0.9526839997 984 -1.136 5.046 4.664 -3.648 4.002 4.442 0.9526834576 999 -1.136 5.046 4.664 -3.647 4.002 4.442 0.9526831152 1000 -1.136 5.046 4.664 -3.647 4.002 4.442 0.9526830807 1003 -1.136 5.046 4.664 -3.647 4.002 4.442 0.9526829216 1013 -1.135 5.046 4.665 -3.647 4.000 4.442 0.9526823575 1015 -1.135 5.046 4.665 -3.647 4.001 4.442 0.9526819899 1016 -1.135 5.046 4.665 -3.647 4.001 4.442 0.9526816840 1017 -1.135 5.046 4.665 -3.647 4.001 4.442 0.9526815133 1021 -1.135 5.046 4.665 -3.647 4.001 4.442 0.9526810144 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 1.028284 1 -25.0 -25.0 25.0 0.959380 2 -25.0 25.0 -25.0 1.049960 3 -25.0 25.0 25.0 1.047398 4 25.0 -25.0 -25.0 1.010401 5 25.0 -25.0 25.0 1.037027 6 25.0 25.0 -25.0 1.037559 7 25.0 25.0 25.0 1.021974 REL: 8 0.952681 8.191983 1.023998 rel = 0.930354 Number of iterations 10 Min cost was 0.952681 Number of FunctionCalls 1023 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.412810 sec Parameters at optimum (transmm) -1.13504 5.04641 4.66491 Parameters at optimum (rotdeg) -3.64696 4.00087 4.44188 Final costs ---------------- Number of surface hits 2399 WM Intensity 269.8859 +/- 114.6629 Ctx Intensity 273.1306 +/- 112.2062 Pct Contrast 2.0605 +/- 45.8248 Cost 0.9527 RelCost 1.9278 Reg at min cost was -0.08154 0.99462 0.06395 -0.13158; 0.99465 0.07712 0.06877 4.08419; -0.06347 -0.06922 0.99558 5.34736; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/002/tmp.bbregister.75343/bbr.pass1.dat, type = 14 Original Reg 0.00017 1.00000 -0.00055 0.87605; 1.00000 -0.00017 0.00000 -1.08237; 0.00000 0.00055 1.00000 0.67792; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.08172 0.00538 -0.06450 1.00763; 0.00535 -0.07730 -0.06877 -5.16655; 0.06347 0.06976 0.00442 -4.66945; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 10.518535 Computing change in rh position Surface-RMS-Diff-mm 9.434062 1.808268 13.558367 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov bold/002/tmp.bbregister.75343/template.nii --init-reg bold/002/tmp.bbregister.75343/bbr.pass1.dat --out-reg bold/002/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/002/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/002/tmp.bbregister.75343/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 mri_segreg --mov bold/002/tmp.bbregister.75343/template.nii --init-reg bold/002/tmp.bbregister.75343/bbr.pass1.dat --out-reg bold/002/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/002/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/002/tmp.bbregister.75343/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/002/tmp.bbregister.75343/template.nii regfile bold/002/tmp.bbregister.75343/bbr.pass1.dat subject 20231006_da047 dof 6 outregfile bold/002/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750419662 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.08154 0.99462 0.06395 -0.13158; 0.99465 0.07712 0.06877 4.08419; -0.06347 -0.06922 0.99558 5.34736; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.038656 1 -25.0 -25.0 25.0 1.012203 2 -25.0 25.0 -25.0 1.041423 3 -25.0 25.0 25.0 1.029611 4 25.0 -25.0 -25.0 1.036571 5 25.0 -25.0 25.0 1.032276 6 25.0 25.0 -25.0 1.013314 7 25.0 25.0 25.0 1.041020 REL: 8 1.024508 8.245075 1.030634 rel = 0.994055 Initial costs ---------------- Number of surface hits 239836 WM Intensity 271.5859 +/- 114.7456 Ctx Intensity 269.2880 +/- 112.9365 Pct Contrast -0.6085 +/- 46.3535 Cost 1.0245 RelCost 0.9941 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.9598 0.9598 0.0 15 -0.1000 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.9588 0.9588 0.0 33 -0.1000 -0.1000 0.0000 -0.1000 0.1000 -0.1000 0.9574 0.9574 0.0 54 -0.1000 -0.1000 0.1000 -0.1000 -0.1000 -0.1000 0.9558 0.9558 0.0 81 -0.1000 0.0000 -0.1000 -0.1000 -0.1000 -0.1000 0.9545 0.9545 0.0 162 -0.1000 0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.9533 0.9533 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.9527 0.9527 0.0 Brute Force -------------------------- Min cost was 0.952681 Number of iterations 729 Search time 1.001165 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 1.024508 2 1.000 0.000 0.000 0.000 0.000 0.000 1.0228885238 6 0.618 0.000 0.000 0.000 0.000 0.000 1.0217679653 8 0.683 0.000 0.000 0.000 0.000 0.000 1.0217000292 10 0.657 0.000 0.000 0.000 0.000 0.000 1.0216517622 11 0.658 0.000 0.000 0.000 0.000 0.000 1.0216505311 12 0.662 0.000 0.000 0.000 0.000 0.000 1.0216473410 14 0.663 0.000 0.000 0.000 0.000 0.000 1.0216468253 15 0.664 0.000 0.000 0.000 0.000 0.000 1.0216467114 25 0.664 0.003 0.000 0.000 0.000 0.000 1.0216413789 27 0.664 0.005 0.000 0.000 0.000 0.000 1.0216411303 31 0.664 0.005 -1.618 0.000 0.000 0.000 1.0097935726 36 0.664 0.005 -1.520 0.000 0.000 0.000 1.0095926500 43 0.664 0.005 -1.521 1.000 0.000 0.000 1.0028188325 46 0.664 0.005 -1.521 1.618 0.000 0.000 1.0026393027 48 0.664 0.005 -1.521 1.331 0.000 0.000 1.0017245706 51 0.664 0.005 -1.521 1.359 0.000 0.000 1.0016747170 53 0.664 0.005 -1.521 1.353 0.000 0.000 1.0016717109 55 0.664 0.005 -1.521 1.352 0.000 0.000 1.0016716703 62 0.664 0.005 -1.521 1.352 -0.618 0.000 0.9984721499 64 0.664 0.005 -1.521 1.352 -0.547 0.000 0.9984051751 66 0.664 0.005 -1.521 1.352 -0.575 0.000 0.9983913653 81 0.664 0.005 -1.521 1.352 -0.576 0.057 0.9981955630 86 0.664 0.005 -1.521 1.352 -0.576 0.056 0.9981950730 powell nthiter 1: fret = 0.998195 97 0.670 0.005 -1.521 1.352 -0.576 0.056 0.9981881897 99 0.681 0.005 -1.521 1.352 -0.576 0.056 0.9981789457 100 0.684 0.005 -1.521 1.352 -0.576 0.056 0.9981786007 102 0.683 0.005 -1.521 1.352 -0.576 0.056 0.9981785152 108 0.683 0.387 -1.521 1.352 -0.576 0.056 0.9961900282 113 0.683 0.389 -1.521 1.352 -0.576 0.056 0.9961861415 114 0.683 0.392 -1.521 1.352 -0.576 0.056 0.9961844016 123 0.683 0.392 -1.674 1.352 -0.576 0.056 0.9961052824 124 0.683 0.392 -1.634 1.352 -0.576 0.056 0.9959583349 125 0.683 0.392 -1.605 1.352 -0.576 0.056 0.9958622895 127 0.683 0.392 -1.601 1.352 -0.576 0.056 0.9958616634 128 0.683 0.392 -1.602 1.352 -0.576 0.056 0.9958615920 135 0.683 0.392 -1.602 1.734 -0.576 0.056 0.9951596033 136 0.683 0.392 -1.602 1.696 -0.576 0.056 0.9951220371 138 0.683 0.392 -1.602 1.694 -0.576 0.056 0.9951184239 139 0.683 0.392 -1.602 1.682 -0.576 0.056 0.9951067601 141 0.683 0.392 -1.602 1.680 -0.576 0.056 0.9951063879 142 0.683 0.392 -1.602 1.679 -0.576 0.056 0.9951062524 154 0.683 0.392 -1.602 1.678 -0.605 0.056 0.9950986835 156 0.683 0.392 -1.602 1.678 -0.593 0.056 0.9950811531 157 0.683 0.392 -1.602 1.678 -0.592 0.056 0.9950798007 158 0.683 0.392 -1.602 1.678 -0.586 0.056 0.9950787136 159 0.683 0.392 -1.602 1.678 -0.588 0.056 0.9950775614 169 0.683 0.392 -1.602 1.678 -0.588 0.059 0.9950687340 170 0.683 0.392 -1.602 1.678 -0.588 0.091 0.9950606797 176 0.683 0.392 -1.602 1.678 -0.588 0.089 0.9950604613 177 0.683 0.392 -1.602 1.678 -0.588 0.090 0.9950604144 178 0.702 0.778 -1.684 2.004 -0.600 0.125 0.9935839821 183 0.713 1.017 -1.735 2.206 -0.608 0.146 0.9931376917 186 0.715 1.052 -1.742 2.235 -0.609 0.150 0.9931020170 188 0.714 1.045 -1.740 2.229 -0.609 0.149 0.9930975675 193 0.714 1.044 -1.740 2.229 -0.609 0.149 0.9930974810 powell nthiter 2: fret = 0.993097 199 1.096 1.044 -1.740 2.229 -0.609 0.149 0.9925515775 200 1.095 1.044 -1.740 2.229 -0.609 0.149 0.9925475750 201 0.956 1.044 -1.740 2.229 -0.609 0.149 0.9924011907 208 0.957 1.044 -1.740 2.229 -0.609 0.149 0.9924006697 215 0.957 1.044 -1.740 2.229 -0.609 0.531 0.9919225995 216 0.957 1.044 -1.740 2.229 -0.609 0.418 0.9915026768 217 0.957 1.044 -1.740 2.229 -0.609 0.374 0.9913346354 218 0.957 1.044 -1.740 2.229 -0.609 0.288 0.9913282496 219 0.957 1.044 -1.740 2.229 -0.609 0.330 0.9912800282 221 0.957 1.044 -1.740 2.229 -0.609 0.346 0.9912688222 223 0.957 1.044 -1.740 2.229 -0.609 0.340 0.9912671592 224 0.957 1.044 -1.740 2.229 -0.609 0.342 0.9912662395 225 0.957 1.044 -1.740 2.229 -0.609 0.343 0.9912661309 231 0.957 1.044 -2.358 2.229 -0.609 0.343 0.9901722544 233 0.957 1.044 -2.125 2.229 -0.609 0.343 0.9889410862 236 0.957 1.044 -2.133 2.229 -0.609 0.343 0.9889236771 237 0.957 1.044 -2.137 2.229 -0.609 0.343 0.9889199709 238 0.957 1.044 -2.139 2.229 -0.609 0.343 0.9889198819 240 0.957 1.044 -2.138 2.229 -0.609 0.343 0.9889197144 247 0.957 1.044 -2.138 2.290 -0.609 0.343 0.9889187018 255 0.957 1.044 -2.138 2.293 -0.609 0.343 0.9889186489 256 0.957 1.044 -2.138 2.292 -0.609 0.343 0.9889185633 266 0.957 1.044 -2.138 2.292 -0.602 0.343 0.9889148816 267 0.957 1.044 -2.138 2.292 -0.604 0.343 0.9889145328 275 0.955 0.998 -2.128 2.252 -0.602 0.339 0.9887780642 276 0.954 0.971 -2.123 2.230 -0.601 0.336 0.9887457470 277 0.953 0.959 -2.120 2.220 -0.601 0.335 0.9887376603 280 0.953 0.949 -2.118 2.212 -0.601 0.334 0.9887298691 281 0.953 0.949 -2.118 2.211 -0.601 0.334 0.9887295099 283 0.953 0.947 -2.118 2.210 -0.601 0.334 0.9887292358 powell nthiter 3: fret = 0.988729 294 0.976 0.947 -2.118 2.210 -0.601 0.334 0.9887132967 295 0.995 0.947 -2.118 2.210 -0.601 0.334 0.9887028059 300 0.993 0.947 -2.118 2.210 -0.601 0.334 0.9887022880 302 0.991 0.947 -2.118 2.210 -0.601 0.334 0.9887020515 313 0.991 0.947 -2.118 2.210 -0.601 0.244 0.9886438972 314 0.991 0.947 -2.118 2.210 -0.601 0.271 0.9885599689 315 0.991 0.947 -2.118 2.210 -0.601 0.283 0.9885497451 317 0.991 0.947 -2.118 2.210 -0.601 0.280 0.9885475658 350 0.991 0.947 -2.118 2.210 -0.614 0.280 0.9885224598 351 0.991 0.947 -2.118 2.210 -0.615 0.280 0.9885222373 361 0.991 0.947 -2.118 2.210 -0.615 0.280 0.9885221319 362 0.991 0.949 -2.118 2.212 -0.615 0.280 0.9885217425 powell nthiter 4: fret = 0.988522 379 0.994 0.951 -2.118 2.213 -0.615 0.280 0.9885217424 381 0.993 0.951 -2.118 2.213 -0.615 0.280 0.9885216625 394 0.993 0.951 -2.118 2.213 -0.615 0.284 0.9885177016 405 0.993 0.951 -2.110 2.213 -0.615 0.284 0.9885085687 417 0.993 0.951 -2.110 2.212 -0.615 0.284 0.9885083718 428 0.993 0.951 -2.110 2.212 -0.619 0.284 0.9885028632 430 0.993 0.951 -2.110 2.212 -0.621 0.284 0.9885022547 441 0.993 0.953 -2.110 2.213 -0.621 0.284 0.9885013122 442 0.993 0.955 -2.111 2.215 -0.621 0.285 0.9885010084 443 0.993 0.954 -2.111 2.215 -0.621 0.284 0.9885009462 444 0.993 0.954 -2.111 2.214 -0.621 0.284 0.9885008894 446 0.995 0.957 -2.103 2.216 -0.626 0.289 0.9884854895 453 0.995 0.957 -2.102 2.216 -0.626 0.289 0.9884854510 454 0.995 0.957 -2.102 2.216 -0.626 0.289 0.9884854329 powell nthiter 5: fret = 0.988485 467 1.000 0.957 -2.102 2.216 -0.626 0.289 0.9884848650 468 0.998 0.957 -2.102 2.216 -0.626 0.289 0.9884839565 483 0.998 0.957 -2.102 2.216 -0.626 0.290 0.9884838576 494 0.998 0.958 -2.102 2.216 -0.626 0.290 0.9884837904 495 0.998 0.958 -2.102 2.217 -0.626 0.290 0.9884837245 498 0.998 0.959 -2.103 2.218 -0.626 0.290 0.9884837077 522 0.998 0.958 -2.102 2.217 -0.627 0.290 0.9884834016 530 0.998 0.958 -2.102 2.217 -0.627 0.290 0.9884833806 532 0.998 0.958 -2.103 2.217 -0.627 0.290 0.9884833547 533 0.998 0.958 -2.103 2.217 -0.627 0.290 0.9884833014 538 0.998 0.958 -2.103 2.217 -0.627 0.290 0.9884832678 powell nthiter 6: fret = 0.988483 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 1.020245 1 -25.0 -25.0 25.0 1.021641 2 -25.0 25.0 -25.0 1.024180 3 -25.0 25.0 25.0 1.013009 4 25.0 -25.0 -25.0 1.040236 5 25.0 -25.0 25.0 1.036301 6 25.0 25.0 -25.0 1.003885 7 25.0 25.0 25.0 1.021881 REL: 8 0.988483 8.181378 1.022672 rel = 0.966569 Number of iterations 6 Min cost was 0.988483 Number of FunctionCalls 616 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 28.481524 sec Parameters at optimum (transmm) 0.99783 0.95822 -2.10294 Parameters at optimum (rotdeg) 2.21701 -0.62711 0.29007 Final costs ---------------- Number of surface hits 239836 WM Intensity 274.1005 +/- 111.8385 Ctx Intensity 276.1199 +/- 112.6135 Pct Contrast 0.5310 +/- 46.5089 Cost 0.9885 RelCost 0.9941 Reg at min cost was -0.08631 0.99486 0.05288 0.78643; 0.99593 0.08478 0.03047 4.83146; -0.02583 -0.05529 0.99814 3.39665; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/002/register.dof6.dat, type = 14 Original Reg -0.08154 0.99462 0.06395 -0.13158; 0.99465 0.07712 0.06877 4.08419; -0.06347 -0.06922 0.99558 5.34736; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00477 -0.00025 0.01107 -0.91801; -0.00129 -0.00766 0.03830 -0.74728; -0.03763 -0.01393 -0.00256 1.95072; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 3.418695 Computing change in rh position Surface-RMS-Diff-mm 2.605381 1.117176 4.872053 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done MinCost: 0.988483 274.100526 276.119916 0.530968 tkregister2_cmdl --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/002/template.nii.gz reg file bold/002/register.dof6.dat LoadVol 0 ZeroCRAS 0 7.4.1 Diagnostic Level -1 ---- Input registration matrix -------- -0.08631 0.99486 0.05288 0.78643; 0.99593 0.08478 0.03047 4.83146; -0.02583 -0.05529 0.99814 3.39665; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/002/template.nii.gz Tmov: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -88.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -0.08631 0.99486 0.05288 0.78643; 0.99593 0.08478 0.03047 4.83146; -0.02583 -0.05529 0.99814 3.39665; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = 20231006_da047 RegMat --------------------------- -0.08631 0.99486 0.05288 0.78643; 0.99593 0.08478 0.03047 4.83146; -0.02583 -0.05529 0.99814 3.39665; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Wed Jun 18 10:06:21 EDT 2025 Ended at Wed Jun 18 10:07:35 EDT 2025 BBR-Run-Time-Sec 74 bbregister Done To check results, run: tkregisterfv --mov bold/002/template.nii.gz --reg bold/002/register.dof6.lta --surfs --sd /Volumes/umms-hillmera/asem_ptsd/DA047 Run: 003 ---------------- Wed Jun 18 10:07:35 EDT 2025 -------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 bbregister --s 20231006_da047 --init-coreg --6 --bold --mov bold/003/template.nii.gz --reg bold/003/register.dof6.dat --lta bold/003/register.dof6.lta --init-reg-out bold/003/init.register.dof6.dat tmp bold/003/tmp.bbregister.75597 Log file is bold/003/register.dof6.log Wed Jun 18 10:07:36 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 /Applications/freesurfer/bin/bbregister --s 20231006_da047 --init-coreg --6 --bold --mov bold/003/template.nii.gz --reg bold/003/register.dof6.dat --lta bold/003/register.dof6.lta --init-reg-out bold/003/init.register.dof6.dat FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 FREESURFER_HOME /Applications/freesurfer mri_convert bold/003/template.nii.gz bold/003/tmp.bbregister.75597/template.nii mri_convert bold/003/template.nii.gz bold/003/tmp.bbregister.75597/template.nii reading from bold/003/template.nii.gz... INFO: This is an unsigined short. TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) writing to bold/003/tmp.bbregister.75597/template.nii... mri_coreg --s 20231006_da047 --mov bold/003/tmp.bbregister.75597/template.nii --regdat bold/003/tmp.bbregister.75597/reg.init.dat --reg bold/003/tmp.bbregister.75597/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 cmdline mri_coreg --s 20231006_da047 --mov bold/003/tmp.bbregister.75597/template.nii --regdat bold/003/tmp.bbregister.75597/reg.init.dat --reg bold/003/tmp.bbregister.75597/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov bold/003/tmp.bbregister.75597/template.nii INFO: This is an unsigined short. Reading in ref /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/brainmask.mgz Reading in and applying refmask /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz Setting cras translation parameters to align volume centers Init matrix params 0.5000 4.0430 -1.8403 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 -0.50000; 0.00000 1.00000 0.00000 -4.04300; 0.00000 0.00000 1.00000 1.84027; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt 0.5000 4.0430 -1.8403 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 3901.3333 mov gstd 1.6917 1.6917 1.6917 Smoothing mov refsat = 115.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0332938704 nhits = 93515 out of 16777216, Percent Overlap: 35.7 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 0.50000; 0.00000 1.00000 0.00000 4.04300; 0.00000 0.00000 1.00000 -1.84027; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.50000 0.00000 0.00000 -9.25000; 0.00000 0.20017 -0.45818 87.39588; 0.00000 -0.45818 -0.20017 115.44038; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -3.50000 30.04300 -11.84027 0.00000 0.00000 0.00000 -1.0402988 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: -3.500000 30.042999 -11.840268 0.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0655981302 #@# 4 188 -3.50000 30.04300 -11.84027 0.00000 0.00000 0.00000 -1.0655981 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.065598 #@# 4 195 -3.65978 30.04300 -11.84027 0.00000 0.00000 0.00000 -1.0656158 #@# 4 196 -3.66983 30.04300 -11.84027 0.00000 0.00000 0.00000 -1.0656173 #@# 4 198 -3.71884 30.04300 -11.84027 0.00000 0.00000 0.00000 -1.0656176 #@# 4 199 -3.69529 30.04300 -11.84027 0.00000 0.00000 0.00000 -1.0656183 #@# 4 204 -3.69529 28.42496 -11.84027 0.00000 0.00000 0.00000 -1.0682073 #@# 4 207 -3.69529 26.59224 -11.84027 0.00000 0.00000 0.00000 -1.0689783 #@# 4 209 -3.69529 26.95257 -11.84027 0.00000 0.00000 0.00000 -1.0690488 #@# 4 210 -3.69529 27.00599 -11.84027 0.00000 0.00000 0.00000 -1.0690511 #@# 4 218 -3.69529 27.00599 -12.45830 0.00000 0.00000 0.00000 -1.0693740 #@# 4 219 -3.69529 27.00599 -12.84027 0.00000 0.00000 0.00000 -1.0693778 #@# 4 220 -3.69529 27.00599 -12.65903 0.00000 0.00000 0.00000 -1.0693932 #@# 4 221 -3.69529 27.00599 -12.66903 0.00000 0.00000 0.00000 -1.0693935 #@# 4 228 -3.69529 27.00599 -12.66903 -0.61803 0.00000 0.00000 -1.0695024 #@# 4 233 -3.69529 27.00599 -12.66903 -0.63092 0.00000 0.00000 -1.0695037 #@# 4 241 -3.69529 27.00599 -12.66903 -0.63092 -0.27233 0.00000 -1.0695167 #@# 4 244 -3.69529 27.00599 -12.66903 -0.63092 -0.33836 0.00000 -1.0695210 powell nthiter 1: fret = -1.069521 #@# 4 267 -3.58697 27.00599 -12.66903 -0.63092 -0.33836 0.00000 -1.0695280 #@# 4 268 -3.59781 27.00599 -12.66903 -0.63092 -0.33836 0.00000 -1.0695293 #@# 4 277 -3.59781 26.78695 -12.66903 -0.63092 -0.33836 0.00000 -1.0695342 #@# 4 278 -3.59781 26.85766 -12.66903 -0.63092 -0.33836 0.00000 -1.0695379 #@# 4 286 -3.59781 26.85766 -12.28707 -0.63092 -0.33836 0.00000 -1.0696044 #@# 4 287 -3.59781 26.85766 -12.31882 -0.63092 -0.33836 0.00000 -1.0696065 #@# 4 288 -3.59781 26.85766 -12.35189 -0.63092 -0.33836 0.00000 -1.0696071 #@# 4 289 -3.59781 26.85766 -12.34189 -0.63092 -0.33836 0.00000 -1.0696075 #@# 4 290 -3.59781 26.85766 -12.33189 -0.63092 -0.33836 0.00000 -1.0696083 #@# 4 298 -3.59781 26.85766 -12.33189 -0.71310 -0.33836 0.00000 -1.0696156 #@# 4 300 -3.59781 26.85766 -12.33189 -0.67971 -0.33836 0.00000 -1.0696161 #@# 4 302 -3.59781 26.85766 -12.33189 -0.68971 -0.33836 0.00000 -1.0696181 #@# 4 320 -3.59781 26.85766 -12.33189 -0.68971 -0.33836 0.16006 -1.0696182 #@# 4 322 -3.59781 26.85766 -12.33189 -0.68971 -0.33836 0.24482 -1.0696217 Powell done niters total = 1 OptTimeSec 5.5 sec OptTimeMin 0.09 min nEvals 327 Final optimized parameters -3.59780884 26.85766411 -12.33189297 -0.68971205 -0.33835638 0.24482268 Final matrix parameters -3.5978 26.8577 -12.3319 -0.6897 -0.3384 0.2548 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.069621733678987 --------------------------------- Final RefRAS-to-MovRAS 0.99997 0.00427 -0.00591 -3.59781; -0.00434 0.99992 -0.01204 26.85766; 0.00585 0.01206 0.99991 -12.33189; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.49999 -0.00295 -0.00214 -6.54798; -0.00082 0.19464 -0.46056 80.16007; -0.00355 -0.46055 -0.19463 106.11459; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters -3.5978 26.8577 -12.3319 -0.6897 -0.3384 0.2448 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters -3.5978 26.8577 -12.3319 -0.6897 -0.3384 0.2448 nhits = 91648 out of 16777216, Percent Overlap: 35.0 mri_coreg RunTimeSec 29.9 sec To check run: tkregisterfv --mov bold/003/tmp.bbregister.75597/template.nii --targ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/brainmask.mgz --reg bold/003/tmp.bbregister.75597/mri_coreg.lta --s 20231006_da047 --surfs mri_coreg done mri_segreg --mov bold/003/tmp.bbregister.75597/template.nii --init-reg bold/003/tmp.bbregister.75597/reg.init.dat --out-reg bold/003/tmp.bbregister.75597/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 mri_segreg --mov bold/003/tmp.bbregister.75597/template.nii --init-reg bold/003/tmp.bbregister.75597/reg.init.dat --out-reg bold/003/tmp.bbregister.75597/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/003/tmp.bbregister.75597/template.nii regfile bold/003/tmp.bbregister.75597/reg.init.dat subject 20231006_da047 dof 6 outregfile bold/003/tmp.bbregister.75597/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750813001 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99997 0.00427 -0.00591 -3.59781; 0.00710 -0.38926 0.92110 -20.40631; -0.00164 0.92112 0.38928 17.96416; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.954354 1 -25.0 -25.0 25.0 1.045694 2 -25.0 25.0 -25.0 1.007321 3 -25.0 25.0 25.0 0.987970 4 25.0 -25.0 -25.0 1.006895 5 25.0 -25.0 25.0 1.029285 6 25.0 25.0 -25.0 1.023123 7 25.0 25.0 25.0 1.021704 REL: 8 1.025982 8.076346 1.009543 rel = 1.01628 Initial costs ---------------- Number of surface hits 2399 WM Intensity 1596.8400 +/- 512.8952 Ctx Intensity 1553.5155 +/- 498.5863 Pct Contrast -2.8118 +/- 22.4646 Cost 1.0260 RelCost 1.0163 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0728 1.0728 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0467 1.0467 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 1.0329 1.0329 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9941 0.9941 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.9757 0.9757 0.0 105 -4.0000 0.0000 -4.0000 4.0000 4.0000 -4.0000 0.9584 0.9584 0.0 256 0.0000 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.9531 0.9531 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.9091 0.9091 0.0 Brute Force -------------------------- Min cost was 0.909099 Number of iterations 729 Search time 0.617649 sec Parameters at best (transmm, rotdeg) 0.000 -4.000 0.000 -4.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -4 2 0 3 -4 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.909099 2 1.000 -4.000 0.000 -4.000 0.000 0.000 0.8882202013 7 0.907 -4.000 0.000 -4.000 0.000 0.000 0.8873621127 9 0.940 -4.000 0.000 -4.000 0.000 0.000 0.8871079371 11 0.935 -4.000 0.000 -4.000 0.000 0.000 0.8870920515 12 0.934 -4.000 0.000 -4.000 0.000 0.000 0.8870912457 16 0.934 -5.618 0.000 -4.000 0.000 0.000 0.8833311507 17 0.934 -5.012 0.000 -4.000 0.000 0.000 0.8818575474 19 0.934 -4.626 0.000 -4.000 0.000 0.000 0.8708925892 21 0.934 -4.666 0.000 -4.000 0.000 0.000 0.8704643570 23 0.934 -4.674 0.000 -4.000 0.000 0.000 0.8704376501 24 0.934 -4.681 0.000 -4.000 0.000 0.000 0.8704343177 27 0.934 -4.680 0.000 -4.000 0.000 0.000 0.8704335520 34 0.934 -4.680 -0.254 -4.000 0.000 0.000 0.8660593913 37 0.934 -4.680 -0.239 -4.000 0.000 0.000 0.8660183068 49 0.934 -4.680 -0.239 -3.954 0.000 0.000 0.8651051930 50 0.934 -4.680 -0.239 -3.949 0.000 0.000 0.8650966109 51 0.934 -4.680 -0.239 -3.948 0.000 0.000 0.8650951445 55 0.934 -4.680 -0.239 -3.947 0.000 0.000 0.8650941345 61 0.934 -4.680 -0.239 -3.947 -0.618 0.000 0.8624094573 63 0.934 -4.680 -0.239 -3.947 -0.726 0.000 0.8604067907 67 0.934 -4.680 -0.239 -3.947 -0.715 0.000 0.8603487486 69 0.934 -4.680 -0.239 -3.947 -0.714 0.000 0.8603483926 78 0.934 -4.680 -0.239 -3.947 -0.714 -0.005 0.8603168954 79 0.934 -4.680 -0.239 -3.947 -0.714 -0.025 0.8602909591 81 0.934 -4.680 -0.239 -3.947 -0.714 -0.018 0.8602834849 82 0.934 -4.680 -0.239 -3.947 -0.714 -0.019 0.8602832731 powell nthiter 1: fret = 0.860283 91 0.896 -4.680 -0.239 -3.947 -0.714 -0.019 0.8601849184 92 0.898 -4.680 -0.239 -3.947 -0.714 -0.019 0.8601567930 93 0.912 -4.680 -0.239 -3.947 -0.714 -0.019 0.8600084215 95 0.913 -4.680 -0.239 -3.947 -0.714 -0.019 0.8600062798 105 0.913 -4.706 -0.239 -3.947 -0.714 -0.019 0.8598948818 106 0.913 -4.698 -0.239 -3.947 -0.714 -0.019 0.8598700057 115 0.913 -4.698 -0.503 -3.947 -0.714 -0.019 0.8582920718 116 0.913 -4.698 -0.504 -3.947 -0.714 -0.019 0.8582898780 117 0.913 -4.698 -0.578 -3.947 -0.714 -0.019 0.8581358039 120 0.913 -4.698 -0.568 -3.947 -0.714 -0.019 0.8581208344 122 0.913 -4.698 -0.564 -3.947 -0.714 -0.019 0.8581167232 132 0.913 -4.698 -0.564 -3.830 -0.714 -0.019 0.8574092659 135 0.913 -4.698 -0.564 -3.849 -0.714 -0.019 0.8571276421 137 0.913 -4.698 -0.564 -3.846 -0.714 -0.019 0.8571079635 139 0.913 -4.698 -0.564 -3.845 -0.714 -0.019 0.8571010004 140 0.913 -4.698 -0.564 -3.843 -0.714 -0.019 0.8570989817 147 0.913 -4.698 -0.564 -3.843 -0.332 -0.019 0.8563787503 148 0.913 -4.698 -0.564 -3.843 -0.479 -0.019 0.8554110568 150 0.913 -4.698 -0.564 -3.843 -0.440 -0.019 0.8552099704 155 0.913 -4.698 -0.564 -3.843 -0.446 -0.019 0.8552075209 156 0.913 -4.698 -0.564 -3.843 -0.445 -0.019 0.8552065120 157 0.913 -4.698 -0.564 -3.843 -0.444 -0.019 0.8552061363 165 0.913 -4.698 -0.564 -3.843 -0.444 0.105 0.8541581790 166 0.913 -4.698 -0.564 -3.843 -0.444 0.133 0.8540013609 168 0.913 -4.698 -0.564 -3.843 -0.444 0.162 0.8539464423 171 0.913 -4.698 -0.564 -3.843 -0.444 0.164 0.8539462725 powell nthiter 2: fret = 0.853946 180 0.941 -4.698 -0.564 -3.843 -0.444 0.164 0.8534033610 181 0.994 -4.698 -0.564 -3.843 -0.444 0.164 0.8523939066 184 1.010 -4.698 -0.564 -3.843 -0.444 0.164 0.8523242250 197 1.010 -4.702 -0.564 -3.843 -0.444 0.164 0.8523191767 206 1.010 -4.702 -0.674 -3.843 -0.444 0.164 0.8501930714 210 1.010 -4.702 -0.675 -3.843 -0.444 0.164 0.8501927952 218 1.010 -4.702 -0.675 -3.782 -0.444 0.164 0.8492411899 220 1.010 -4.702 -0.675 -3.773 -0.444 0.164 0.8491659592 221 1.010 -4.702 -0.675 -3.766 -0.444 0.164 0.8491257278 223 1.010 -4.702 -0.675 -3.762 -0.444 0.164 0.8491180000 224 1.010 -4.702 -0.675 -3.761 -0.444 0.164 0.8491168480 235 1.010 -4.702 -0.675 -3.761 -0.453 0.164 0.8490931675 236 1.010 -4.702 -0.675 -3.761 -0.455 0.164 0.8490926165 245 1.010 -4.702 -0.675 -3.761 -0.455 0.233 0.8487610681 248 1.010 -4.702 -0.675 -3.761 -0.455 0.263 0.8487077197 251 1.010 -4.702 -0.675 -3.761 -0.455 0.256 0.8486999892 253 1.010 -4.702 -0.675 -3.761 -0.455 0.258 0.8486972923 255 1.010 -4.702 -0.675 -3.761 -0.455 0.257 0.8486972915 powell nthiter 3: fret = 0.848697 264 1.009 -4.702 -0.675 -3.761 -0.455 0.257 0.8486919738 266 1.008 -4.702 -0.675 -3.761 -0.455 0.257 0.8486918766 274 1.008 -4.708 -0.675 -3.761 -0.455 0.257 0.8486201457 275 1.008 -4.744 -0.675 -3.761 -0.455 0.257 0.8485491065 277 1.008 -4.738 -0.675 -3.761 -0.455 0.257 0.8485376029 278 1.008 -4.734 -0.675 -3.761 -0.455 0.257 0.8485293602 282 1.008 -4.733 -0.675 -3.761 -0.455 0.257 0.8485293456 292 1.008 -4.733 -0.652 -3.761 -0.455 0.257 0.8484291446 293 1.008 -4.733 -0.650 -3.761 -0.455 0.257 0.8484290846 302 1.008 -4.733 -0.649 -3.737 -0.455 0.257 0.8483566189 304 1.008 -4.733 -0.649 -3.743 -0.455 0.257 0.8483553953 305 1.008 -4.733 -0.649 -3.740 -0.455 0.257 0.8483526563 316 1.008 -4.733 -0.649 -3.740 -0.473 0.257 0.8483474459 317 1.008 -4.733 -0.649 -3.740 -0.465 0.257 0.8483374288 319 1.008 -4.733 -0.649 -3.740 -0.466 0.257 0.8483369237 321 1.008 -4.733 -0.649 -3.740 -0.467 0.257 0.8483364632 329 1.008 -4.733 -0.649 -3.740 -0.467 0.293 0.8481853937 333 1.005 -4.763 -0.623 -3.719 -0.480 0.329 0.8479238193 341 1.005 -4.763 -0.623 -3.720 -0.479 0.328 0.8479237681 350 1.005 -4.762 -0.623 -3.720 -0.479 0.328 0.8479235613 powell nthiter 4: fret = 0.847924 359 1.004 -4.762 -0.623 -3.720 -0.479 0.328 0.8479230278 360 1.003 -4.762 -0.623 -3.720 -0.479 0.328 0.8479228630 370 1.003 -4.762 -0.623 -3.720 -0.479 0.317 0.8478395161 371 1.003 -4.762 -0.623 -3.720 -0.479 0.299 0.8477841335 372 1.003 -4.762 -0.623 -3.720 -0.479 0.297 0.8477839610 382 1.003 -4.762 -0.622 -3.720 -0.479 0.297 0.8477822203 383 1.003 -4.762 -0.619 -3.720 -0.479 0.297 0.8477784196 387 1.003 -4.762 -0.618 -3.720 -0.479 0.297 0.8477781653 394 1.003 -4.762 -0.618 -3.718 -0.479 0.297 0.8477700531 395 1.003 -4.762 -0.618 -3.693 -0.479 0.297 0.8477617395 397 1.003 -4.762 -0.618 -3.704 -0.479 0.297 0.8477387862 398 1.003 -4.762 -0.618 -3.705 -0.479 0.297 0.8477386311 407 1.003 -4.762 -0.618 -3.705 -0.485 0.297 0.8477104350 408 1.003 -4.762 -0.618 -3.705 -0.498 0.297 0.8476813939 410 1.003 -4.762 -0.618 -3.705 -0.496 0.297 0.8476810305 413 1.003 -4.762 -0.618 -3.705 -0.497 0.297 0.8476803497 415 1.000 -4.793 -0.592 -3.684 -0.509 0.333 0.8473199870 420 1.000 -4.798 -0.588 -3.681 -0.511 0.339 0.8473116959 421 1.000 -4.798 -0.588 -3.681 -0.511 0.339 0.8473110644 powell nthiter 5: fret = 0.847311 439 0.983 -4.798 -0.588 -3.681 -0.511 0.339 0.8472242855 440 0.982 -4.798 -0.588 -3.681 -0.511 0.339 0.8472241826 449 0.982 -4.798 -0.588 -3.681 -0.511 0.324 0.8471311953 450 0.982 -4.798 -0.588 -3.681 -0.511 0.311 0.8470694665 452 0.982 -4.798 -0.588 -3.681 -0.511 0.303 0.8470606218 463 0.982 -4.798 -0.602 -3.681 -0.511 0.303 0.8470192635 464 0.982 -4.798 -0.601 -3.681 -0.511 0.303 0.8470189881 465 0.982 -4.798 -0.600 -3.681 -0.511 0.303 0.8470188420 477 0.982 -4.798 -0.600 -3.660 -0.511 0.303 0.8468830552 489 0.982 -4.798 -0.600 -3.660 -0.517 0.303 0.8468680099 492 0.982 -4.798 -0.600 -3.660 -0.520 0.303 0.8468659978 500 0.981 -4.810 -0.590 -3.652 -0.525 0.317 0.8467997037 501 0.982 -4.808 -0.592 -3.653 -0.524 0.315 0.8467981560 503 0.982 -4.809 -0.592 -3.653 -0.524 0.315 0.8467979833 powell nthiter 6: fret = 0.846798 514 0.974 -4.809 -0.592 -3.653 -0.524 0.315 0.8467778392 525 0.974 -4.809 -0.592 -3.653 -0.524 0.299 0.8467310945 527 0.974 -4.809 -0.592 -3.653 -0.524 0.294 0.8467283683 528 0.974 -4.809 -0.592 -3.653 -0.524 0.295 0.8467281270 538 0.974 -4.809 -0.599 -3.653 -0.524 0.295 0.8467190712 539 0.974 -4.809 -0.598 -3.653 -0.524 0.295 0.8467185388 550 0.974 -4.809 -0.598 -3.652 -0.524 0.295 0.8467185163 560 0.974 -4.809 -0.598 -3.652 -0.523 0.295 0.8467173907 568 0.973 -4.813 -0.594 -3.648 -0.525 0.300 0.8466992474 570 0.973 -4.812 -0.595 -3.649 -0.525 0.299 0.8466975657 572 0.974 -4.812 -0.595 -3.649 -0.524 0.299 0.8466971097 573 0.974 -4.812 -0.595 -3.649 -0.524 0.298 0.8466968870 577 0.974 -4.812 -0.595 -3.649 -0.524 0.299 0.8466968772 578 0.974 -4.812 -0.595 -3.649 -0.524 0.299 0.8466967542 powell nthiter 7: fret = 0.846697 589 0.973 -4.812 -0.595 -3.649 -0.524 0.299 0.8466965429 598 0.973 -4.812 -0.595 -3.649 -0.524 0.296 0.8466949885 599 0.973 -4.812 -0.595 -3.649 -0.524 0.295 0.8466949851 600 0.973 -4.812 -0.595 -3.649 -0.524 0.294 0.8466945250 614 0.973 -4.812 -0.599 -3.649 -0.524 0.292 0.8466901756 626 0.973 -4.812 -0.599 -3.651 -0.524 0.292 0.8466890139 636 0.973 -4.812 -0.599 -3.651 -0.523 0.292 0.8466878858 637 0.973 -4.812 -0.599 -3.651 -0.522 0.292 0.8466871030 645 0.972 -4.816 -0.595 -3.648 -0.523 0.297 0.8466766603 646 0.972 -4.816 -0.596 -3.648 -0.523 0.296 0.8466757521 647 0.972 -4.815 -0.596 -3.649 -0.523 0.295 0.8466754211 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 0.985902 1 -25.0 -25.0 25.0 1.009711 2 -25.0 25.0 -25.0 1.000220 3 -25.0 25.0 25.0 0.959065 4 25.0 -25.0 -25.0 0.991505 5 25.0 -25.0 25.0 1.023085 6 25.0 25.0 -25.0 0.993725 7 25.0 25.0 25.0 0.988473 REL: 8 0.846675 7.951685 0.993961 rel = 0.85182 Number of iterations 7 Min cost was 0.846675 Number of FunctionCalls 656 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.558185 sec Parameters at optimum (transmm) 0.97226 -4.81504 -0.59616 Parameters at optimum (rotdeg) -3.64887 -0.52296 0.29543 Final costs ---------------- Number of surface hits 2399 WM Intensity 1484.5028 +/- 483.8671 Ctx Intensity 1517.7412 +/- 513.4250 Pct Contrast 1.6994 +/- 21.8035 Cost 0.8467 RelCost 1.0163 Reg at min cost was 0.99990 -0.00264 -0.01378 -2.70172; 0.01214 -0.32987 0.94395 -24.05591; 0.00704 0.94402 0.32981 18.59664; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/003/tmp.bbregister.75597/bbr.pass1.dat, type = 14 Original Reg 0.99997 0.00427 -0.00591 -3.59781; 0.00710 -0.38926 0.92110 -20.40631; -0.00164 0.92112 0.38928 17.96416; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00007 0.00692 0.00788 -0.89608; -0.00504 -0.05939 -0.02285 3.64960; -0.00868 -0.02291 0.05948 -0.63248; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 5.536754 Computing change in rh position Surface-RMS-Diff-mm 5.517454 2.442223 10.379261 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov bold/003/tmp.bbregister.75597/template.nii --init-reg bold/003/tmp.bbregister.75597/bbr.pass1.dat --out-reg bold/003/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/003/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/003/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/003/tmp.bbregister.75597/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 mri_segreg --mov bold/003/tmp.bbregister.75597/template.nii --init-reg bold/003/tmp.bbregister.75597/bbr.pass1.dat --out-reg bold/003/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/003/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/003/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/003/tmp.bbregister.75597/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/003/tmp.bbregister.75597/template.nii regfile bold/003/tmp.bbregister.75597/bbr.pass1.dat subject 20231006_da047 dof 6 outregfile bold/003/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750844053 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99990 -0.00264 -0.01378 -2.70172; 0.01214 -0.32987 0.94395 -24.05591; 0.00704 0.94402 0.32981 18.59664; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.989135 1 -25.0 -25.0 25.0 1.008497 2 -25.0 25.0 -25.0 0.997781 3 -25.0 25.0 25.0 0.977911 4 25.0 -25.0 -25.0 1.001505 5 25.0 -25.0 25.0 1.013390 6 25.0 25.0 -25.0 0.982096 7 25.0 25.0 25.0 1.002548 REL: 8 0.892574 7.972863 0.996608 rel = 0.895613 Initial costs ---------------- Number of surface hits 239836 WM Intensity 1486.5861 +/- 480.5222 Ctx Intensity 1513.1268 +/- 501.9602 Pct Contrast 1.2456 +/- 22.5171 Cost 0.8926 RelCost 0.8956 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.8562 0.8562 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.8542 0.8542 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.8530 0.8530 0.0 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.8523 0.8523 0.0 84 -0.1000 0.0000 -0.1000 -0.1000 0.0000 -0.1000 0.8519 0.8519 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.8506 0.8506 0.0 117 -0.1000 0.0000 0.0000 0.0000 -0.1000 -0.1000 0.8504 0.8504 0.0 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.8490 0.8490 0.0 283 0.0000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.8489 0.8489 0.0 337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.8485 0.8485 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.8479 0.8479 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.8467 0.8467 0.0 Brute Force -------------------------- Min cost was 0.846675 Number of iterations 729 Search time 0.610018 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.892574 7 -0.067 0.000 0.000 0.000 0.000 0.000 0.8924227147 9 -0.091 0.000 0.000 0.000 0.000 0.000 0.8924100455 11 -0.095 0.000 0.000 0.000 0.000 0.000 0.8924087881 12 -0.117 0.000 0.000 0.000 0.000 0.000 0.8923998646 17 -0.115 0.000 0.000 0.000 0.000 0.000 0.8923998190 21 -0.115 1.000 0.000 0.000 0.000 0.000 0.8898627514 25 -0.115 0.618 0.000 0.000 0.000 0.000 0.8892590584 27 -0.115 0.635 0.000 0.000 0.000 0.000 0.8892409125 28 -0.115 0.647 0.000 0.000 0.000 0.000 0.8892351030 30 -0.115 0.648 0.000 0.000 0.000 0.000 0.8892350836 34 -0.115 0.648 -1.618 0.000 0.000 0.000 0.8869538934 35 -0.115 0.648 -0.877 0.000 0.000 0.000 0.8793973368 39 -0.115 0.648 -0.940 0.000 0.000 0.000 0.8793094298 40 -0.115 0.648 -0.944 0.000 0.000 0.000 0.8793077261 41 -0.115 0.648 -0.957 0.000 0.000 0.000 0.8793076953 43 -0.115 0.648 -0.951 0.000 0.000 0.000 0.8793069238 46 -0.115 0.648 -0.950 0.000 0.000 0.000 0.8793068785 48 -0.115 0.648 -0.950 1.000 0.000 0.000 0.8747791252 51 -0.115 0.648 -0.950 1.618 0.000 0.000 0.8733198972 55 -0.115 0.648 -0.950 1.559 0.000 0.000 0.8732982009 57 -0.115 0.648 -0.950 1.582 0.000 0.000 0.8732847053 58 -0.115 0.648 -0.950 1.581 0.000 0.000 0.8732842278 59 -0.115 0.648 -0.950 1.577 0.000 0.000 0.8732833583 70 -0.115 0.648 -0.950 1.579 0.132 0.000 0.8723256682 71 -0.115 0.648 -0.950 1.579 0.161 0.000 0.8722757459 72 -0.115 0.648 -0.950 1.579 0.172 0.000 0.8722757130 73 -0.115 0.648 -0.950 1.579 0.166 0.000 0.8722741360 81 -0.115 0.648 -0.950 1.579 0.167 -0.618 0.8698873854 83 -0.115 0.648 -0.950 1.579 0.167 -0.492 0.8695286415 84 -0.115 0.648 -0.950 1.579 0.167 -0.451 0.8694855826 88 -0.115 0.648 -0.950 1.579 0.167 -0.450 0.8694854639 powell nthiter 1: fret = 0.869485 99 -0.062 0.648 -0.950 1.579 0.167 -0.450 0.8694706991 100 -0.085 0.648 -0.950 1.579 0.167 -0.450 0.8694429982 109 -0.085 0.500 -0.950 1.579 0.167 -0.450 0.8692339511 110 -0.085 0.509 -0.950 1.579 0.167 -0.450 0.8692242091 111 -0.085 0.534 -0.950 1.579 0.167 -0.450 0.8691994362 113 -0.085 0.544 -0.950 1.579 0.167 -0.450 0.8691984544 117 -0.085 0.546 -0.950 1.579 0.167 -0.450 0.8691982306 123 -0.085 0.546 -1.568 1.579 0.167 -0.450 0.8686072866 125 -0.085 0.546 -1.296 1.579 0.167 -0.450 0.8680938313 126 -0.085 0.546 -1.317 1.579 0.167 -0.450 0.8680812855 127 -0.085 0.546 -1.337 1.579 0.167 -0.450 0.8680804742 128 -0.085 0.546 -1.329 1.579 0.167 -0.450 0.8680794704 129 -0.085 0.546 -1.330 1.579 0.167 -0.450 0.8680794229 138 -0.085 0.546 -1.330 1.588 0.167 -0.450 0.8680677277 139 -0.085 0.546 -1.330 1.610 0.167 -0.450 0.8680529287 141 -0.085 0.546 -1.330 1.607 0.167 -0.450 0.8680529158 143 -0.085 0.546 -1.330 1.608 0.167 -0.450 0.8680527162 151 -0.085 0.546 -1.330 1.608 0.177 -0.450 0.8680389885 153 -0.085 0.546 -1.330 1.608 0.232 -0.450 0.8680295291 154 -0.085 0.546 -1.330 1.608 0.209 -0.450 0.8680051895 156 -0.085 0.546 -1.330 1.608 0.210 -0.450 0.8680050638 167 -0.085 0.546 -1.330 1.608 0.210 -0.509 0.8679722872 168 -0.085 0.546 -1.330 1.608 0.210 -0.505 0.8679704068 169 -0.085 0.546 -1.330 1.608 0.210 -0.494 0.8679688754 171 -0.085 0.546 -1.330 1.608 0.210 -0.497 0.8679687852 172 -0.085 0.546 -1.330 1.608 0.210 -0.498 0.8679687692 173 -0.085 0.546 -1.330 1.608 0.210 -0.499 0.8679687148 182 -0.074 0.507 -1.475 1.620 0.226 -0.517 0.8677777804 183 -0.069 0.492 -1.532 1.624 0.233 -0.525 0.8677690224 184 -0.070 0.496 -1.517 1.623 0.231 -0.523 0.8677525096 185 -0.071 0.499 -1.506 1.622 0.230 -0.522 0.8677522011 186 -0.071 0.497 -1.511 1.623 0.230 -0.522 0.8677512721 187 -0.071 0.498 -1.511 1.623 0.230 -0.522 0.8677510902 powell nthiter 2: fret = 0.867751 196 -0.027 0.498 -1.511 1.623 0.230 -0.522 0.8676643759 198 -0.029 0.498 -1.511 1.623 0.230 -0.522 0.8676640850 204 -0.028 -0.120 -1.511 1.623 0.230 -0.522 0.8676549876 206 -0.028 0.186 -1.511 1.623 0.230 -0.522 0.8669003924 207 -0.028 0.188 -1.511 1.623 0.230 -0.522 0.8668975521 209 -0.028 0.243 -1.511 1.623 0.230 -0.522 0.8668945043 210 -0.028 0.216 -1.511 1.623 0.230 -0.522 0.8668759201 212 -0.028 0.205 -1.511 1.623 0.230 -0.522 0.8668745175 213 -0.028 0.209 -1.511 1.623 0.230 -0.522 0.8668727138 222 -0.028 0.209 -1.511 1.623 0.230 -0.666 0.8668514954 223 -0.028 0.209 -1.511 1.623 0.230 -0.606 0.8668267800 225 -0.028 0.209 -1.511 1.623 0.230 -0.621 0.8668225875 227 -0.028 0.209 -1.511 1.623 0.230 -0.627 0.8668219743 229 -0.028 0.209 -1.511 1.623 0.230 -0.626 0.8668219580 236 -0.028 0.209 -1.511 2.004 0.230 -0.626 0.8658602732 237 -0.028 0.209 -1.511 1.989 0.230 -0.626 0.8658560449 249 -0.028 0.209 -1.511 1.989 0.232 -0.626 0.8658558504 250 -0.028 0.209 -1.511 1.989 0.233 -0.626 0.8658558011 259 -0.017 0.170 -1.656 2.001 0.250 -0.644 0.8658074826 260 -0.020 0.182 -1.613 1.997 0.245 -0.639 0.8658018674 261 -0.020 0.180 -1.620 1.998 0.246 -0.640 0.8658011855 262 -0.019 0.179 -1.624 1.998 0.246 -0.640 0.8658008888 265 -0.019 0.179 -1.625 1.998 0.246 -0.640 0.8658008862 266 -0.019 0.178 -1.628 1.999 0.247 -0.641 0.8658008728 270 0.047 -0.191 -1.927 2.389 0.283 -0.783 0.8648763584 276 0.022 -0.050 -1.813 2.240 0.269 -0.729 0.8645475255 278 0.019 -0.036 -1.802 2.225 0.268 -0.723 0.8645172438 279 0.016 -0.016 -1.786 2.204 0.266 -0.716 0.8645095917 280 0.017 -0.022 -1.791 2.210 0.266 -0.718 0.8645069443 281 0.017 -0.023 -1.791 2.211 0.266 -0.718 0.8645066606 283 0.017 -0.024 -1.792 2.213 0.267 -0.719 0.8645064591 284 0.017 -0.024 -1.792 2.212 0.267 -0.719 0.8645064559 powell nthiter 3: fret = 0.864506 292 0.191 -0.024 -1.792 2.212 0.267 -0.719 0.8636753689 293 0.188 -0.024 -1.792 2.212 0.267 -0.719 0.8636740197 294 0.183 -0.024 -1.792 2.212 0.267 -0.719 0.8636728939 297 0.182 -0.024 -1.792 2.212 0.267 -0.719 0.8636726088 298 0.181 -0.024 -1.792 2.212 0.267 -0.719 0.8636725725 306 0.181 -0.330 -1.792 2.212 0.267 -0.719 0.8629077107 307 0.181 -0.328 -1.792 2.212 0.267 -0.719 0.8629063524 308 0.181 -0.288 -1.792 2.212 0.267 -0.719 0.8629047082 310 0.181 -0.307 -1.792 2.212 0.267 -0.719 0.8628933504 311 0.181 -0.308 -1.792 2.212 0.267 -0.719 0.8628932110 312 0.181 -0.310 -1.792 2.212 0.267 -0.719 0.8628932088 315 0.181 -0.309 -1.792 2.212 0.267 -0.719 0.8628931178 321 0.181 -0.309 -1.792 2.212 0.267 -0.337 0.8628561304 322 0.181 -0.309 -1.792 2.212 0.267 -0.513 0.8627463877 323 0.181 -0.309 -1.792 2.212 0.267 -0.514 0.8627454617 324 0.181 -0.309 -1.792 2.212 0.267 -0.592 0.8626850425 326 0.181 -0.309 -1.792 2.212 0.267 -0.580 0.8626836300 327 0.181 -0.309 -1.792 2.212 0.267 -0.582 0.8626835440 336 0.181 -0.308 -1.787 2.212 0.266 -0.582 0.8626809791 337 0.180 -0.305 -1.777 2.211 0.265 -0.580 0.8626803624 339 0.180 -0.306 -1.781 2.211 0.265 -0.581 0.8626798085 340 0.180 -0.306 -1.781 2.211 0.265 -0.581 0.8626797615 342 0.180 -0.306 -1.779 2.211 0.265 -0.581 0.8626797592 345 0.180 -0.306 -1.780 2.211 0.265 -0.581 0.8626797038 352 0.180 -0.306 -1.780 2.211 0.269 -0.581 0.8626796093 353 0.180 -0.306 -1.780 2.211 0.268 -0.581 0.8626794645 356 0.246 -0.674 -2.079 2.601 0.303 -0.723 0.8626523219 360 0.221 -0.534 -1.965 2.452 0.289 -0.669 0.8622624151 361 0.220 -0.527 -1.960 2.445 0.288 -0.666 0.8622503075 363 0.215 -0.500 -1.937 2.416 0.286 -0.655 0.8622288491 364 0.215 -0.501 -1.938 2.418 0.286 -0.656 0.8622276913 365 0.216 -0.508 -1.944 2.425 0.286 -0.659 0.8622262342 367 0.216 -0.505 -1.942 2.422 0.286 -0.658 0.8622258003 368 0.216 -0.506 -1.942 2.423 0.286 -0.658 0.8622256798 369 0.216 -0.506 -1.942 2.423 0.286 -0.658 0.8622255620 powell nthiter 4: fret = 0.862226 378 0.363 -0.506 -1.942 2.423 0.286 -0.658 0.8617884764 379 0.355 -0.506 -1.942 2.423 0.286 -0.658 0.8617728370 380 0.330 -0.506 -1.942 2.423 0.286 -0.658 0.8617355827 383 0.324 -0.506 -1.942 2.423 0.286 -0.658 0.8617324498 384 0.322 -0.506 -1.942 2.423 0.286 -0.658 0.8617323698 385 0.321 -0.506 -1.942 2.423 0.286 -0.658 0.8617323676 397 0.321 -0.508 -1.942 2.423 0.286 -0.658 0.8617320835 405 0.321 -0.508 -1.942 2.423 0.286 -0.622 0.8616515157 406 0.321 -0.508 -1.942 2.423 0.286 -0.540 0.8616002786 408 0.321 -0.508 -1.942 2.423 0.286 -0.543 0.8615998786 409 0.321 -0.508 -1.942 2.423 0.286 -0.545 0.8615998067 410 0.321 -0.508 -1.942 2.423 0.286 -0.546 0.8615997841 411 0.321 -0.508 -1.942 2.423 0.286 -0.547 0.8615997558 418 0.302 -0.445 -1.708 2.405 0.260 -0.517 0.8612512432 420 0.308 -0.462 -1.772 2.410 0.267 -0.525 0.8610709230 422 0.308 -0.464 -1.779 2.410 0.268 -0.526 0.8610701258 425 0.308 -0.464 -1.779 2.410 0.268 -0.526 0.8610700092 433 0.308 -0.464 -1.779 2.410 0.277 -0.526 0.8610607981 434 0.308 -0.464 -1.779 2.410 0.295 -0.526 0.8610570927 436 0.308 -0.464 -1.779 2.410 0.289 -0.526 0.8610563127 437 0.308 -0.464 -1.779 2.410 0.290 -0.526 0.8610562924 438 0.308 -0.464 -1.779 2.410 0.291 -0.526 0.8610562276 445 0.333 -0.604 -1.893 2.559 0.305 -0.581 0.8610077187 446 0.322 -0.543 -1.843 2.494 0.299 -0.557 0.8609881412 447 0.324 -0.555 -1.853 2.507 0.300 -0.561 0.8609825821 448 0.326 -0.564 -1.860 2.516 0.301 -0.565 0.8609783972 450 0.327 -0.567 -1.863 2.520 0.302 -0.566 0.8609779959 451 0.327 -0.568 -1.863 2.520 0.302 -0.566 0.8609779177 455 0.438 -0.629 -1.784 2.618 0.317 -0.475 0.8604612597 460 0.506 -0.667 -1.735 2.678 0.326 -0.418 0.8603522245 462 0.484 -0.655 -1.751 2.658 0.323 -0.436 0.8603166854 464 0.486 -0.656 -1.749 2.660 0.324 -0.434 0.8603159093 467 0.487 -0.656 -1.748 2.661 0.324 -0.434 0.8603157921 468 0.487 -0.657 -1.748 2.661 0.324 -0.434 0.8603157595 powell nthiter 5: fret = 0.860316 477 0.455 -0.657 -1.748 2.661 0.324 -0.434 0.8603065729 478 0.466 -0.657 -1.748 2.661 0.324 -0.434 0.8603017343 488 0.465 -0.598 -1.748 2.661 0.324 -0.434 0.8600378779 490 0.465 -0.569 -1.748 2.661 0.324 -0.434 0.8599915745 491 0.465 -0.568 -1.748 2.661 0.324 -0.434 0.8599913910 492 0.465 -0.566 -1.748 2.661 0.324 -0.434 0.8599913111 502 0.465 -0.565 -1.748 2.661 0.324 -0.381 0.8599760771 503 0.465 -0.565 -1.748 2.661 0.324 -0.397 0.8599707308 504 0.465 -0.565 -1.748 2.661 0.324 -0.399 0.8599703168 505 0.465 -0.565 -1.748 2.661 0.324 -0.412 0.8599694678 506 0.465 -0.565 -1.748 2.661 0.324 -0.407 0.8599689272 517 0.466 -0.574 -1.755 2.670 0.325 -0.411 0.8599598049 518 0.466 -0.576 -1.757 2.672 0.325 -0.411 0.8599593812 519 0.467 -0.576 -1.757 2.673 0.325 -0.412 0.8599591723 522 0.467 -0.577 -1.758 2.673 0.325 -0.412 0.8599591384 530 0.467 -0.577 -1.758 2.673 0.258 -0.412 0.8599430351 531 0.467 -0.577 -1.758 2.673 0.286 -0.412 0.8599121140 532 0.467 -0.577 -1.758 2.673 0.288 -0.412 0.8599114567 534 0.467 -0.577 -1.758 2.673 0.292 -0.412 0.8599109267 536 0.467 -0.577 -1.758 2.673 0.293 -0.412 0.8599109192 544 0.476 -0.582 -1.751 2.681 0.294 -0.404 0.8599025065 546 0.475 -0.582 -1.751 2.681 0.294 -0.405 0.8599024615 powell nthiter 6: fret = 0.859902 558 0.458 -0.582 -1.751 2.681 0.294 -0.405 0.8599022665 559 0.467 -0.582 -1.751 2.681 0.294 -0.405 0.8598980574 561 0.466 -0.582 -1.751 2.681 0.294 -0.405 0.8598980168 572 0.466 -0.569 -1.751 2.681 0.294 -0.405 0.8598975248 573 0.466 -0.575 -1.751 2.681 0.294 -0.405 0.8598966059 574 0.466 -0.574 -1.751 2.681 0.294 -0.405 0.8598965268 575 0.466 -0.573 -1.751 2.681 0.294 -0.405 0.8598964948 586 0.466 -0.573 -1.751 2.681 0.294 -0.415 0.8598959521 588 0.466 -0.573 -1.751 2.681 0.294 -0.411 0.8598953059 590 0.466 -0.573 -1.751 2.681 0.294 -0.412 0.8598952583 600 0.467 -0.577 -1.755 2.686 0.295 -0.413 0.8598939351 601 0.466 -0.577 -1.755 2.685 0.295 -0.413 0.8598939305 602 0.466 -0.577 -1.754 2.685 0.295 -0.413 0.8598938401 612 0.466 -0.577 -1.754 2.685 0.288 -0.413 0.8598922289 621 0.474 -0.581 -1.749 2.692 0.289 -0.406 0.8598871493 623 0.473 -0.580 -1.750 2.690 0.289 -0.408 0.8598866657 629 0.472 -0.580 -1.750 2.690 0.289 -0.408 0.8598866388 631 0.469 -0.578 -1.749 2.699 0.283 -0.412 0.8598777914 634 0.464 -0.575 -1.747 2.713 0.275 -0.417 0.8598682415 635 0.458 -0.571 -1.744 2.729 0.265 -0.424 0.8598620602 640 0.458 -0.571 -1.744 2.731 0.264 -0.424 0.8598619044 641 0.458 -0.571 -1.744 2.731 0.264 -0.425 0.8598618491 643 0.458 -0.571 -1.744 2.732 0.264 -0.425 0.8598618454 644 0.458 -0.571 -1.744 2.731 0.264 -0.425 0.8598618230 646 0.458 -0.571 -1.744 2.731 0.264 -0.425 0.8598618216 648 0.458 -0.571 -1.744 2.731 0.264 -0.425 0.8598617984 powell nthiter 7: fret = 0.859862 655 0.479 -0.571 -1.744 2.731 0.264 -0.425 0.8598396791 657 0.477 -0.571 -1.744 2.731 0.264 -0.425 0.8598393552 667 0.476 -0.546 -1.744 2.731 0.264 -0.425 0.8598281959 668 0.476 -0.547 -1.744 2.731 0.264 -0.425 0.8598274056 669 0.476 -0.554 -1.744 2.731 0.264 -0.425 0.8598258294 671 0.476 -0.552 -1.744 2.731 0.264 -0.425 0.8598255939 683 0.476 -0.551 -1.744 2.731 0.264 -0.421 0.8598253234 687 0.476 -0.551 -1.744 2.731 0.264 -0.420 0.8598252595 695 0.480 -0.568 -1.758 2.749 0.265 -0.427 0.8598180268 696 0.478 -0.562 -1.753 2.743 0.265 -0.424 0.8598115680 697 0.478 -0.561 -1.752 2.742 0.265 -0.424 0.8598114268 698 0.478 -0.561 -1.752 2.742 0.265 -0.424 0.8598113651 710 0.478 -0.561 -1.752 2.742 0.273 -0.424 0.8598061128 711 0.478 -0.561 -1.752 2.742 0.274 -0.424 0.8598060367 712 0.478 -0.561 -1.752 2.742 0.275 -0.424 0.8598059485 716 0.475 -0.559 -1.751 2.751 0.270 -0.427 0.8598056384 720 0.476 -0.560 -1.751 2.747 0.272 -0.426 0.8598047784 723 0.476 -0.560 -1.751 2.747 0.272 -0.426 0.8598047688 powell nthiter 8: fret = 0.859805 738 0.478 -0.560 -1.751 2.747 0.272 -0.426 0.8598043481 740 0.479 -0.560 -1.751 2.747 0.272 -0.426 0.8598043455 749 0.479 -0.551 -1.751 2.747 0.272 -0.426 0.8598008727 761 0.479 -0.550 -1.751 2.747 0.272 -0.420 0.8597992050 773 0.479 -0.552 -1.752 2.749 0.272 -0.420 0.8597983298 774 0.480 -0.553 -1.753 2.750 0.272 -0.421 0.8597981687 775 0.480 -0.552 -1.753 2.750 0.272 -0.421 0.8597981657 785 0.480 -0.552 -1.753 2.750 0.274 -0.421 0.8597975507 786 0.480 -0.552 -1.753 2.750 0.276 -0.421 0.8597975167 794 0.479 -0.552 -1.753 2.751 0.275 -0.421 0.8597973723 795 0.479 -0.552 -1.753 2.751 0.275 -0.421 0.8597973333 powell nthiter 9: fret = 0.859797 820 0.480 -0.551 -1.753 2.751 0.275 -0.421 0.8597970643 822 0.480 -0.550 -1.753 2.751 0.275 -0.421 0.8597969584 843 0.480 -0.551 -1.754 2.752 0.275 -0.420 0.8597969566 846 0.480 -0.551 -1.753 2.751 0.275 -0.419 0.8597968227 856 0.480 -0.551 -1.753 2.751 0.276 -0.419 0.8597968192 866 0.480 -0.551 -1.753 2.751 0.276 -0.419 0.8597967690 powell nthiter 10: fret = 0.859797 880 0.479 -0.551 -1.753 2.752 0.276 -0.419 0.8597967528 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 0.991042 1 -25.0 -25.0 25.0 1.024453 2 -25.0 25.0 -25.0 0.989333 3 -25.0 25.0 25.0 0.977691 4 25.0 -25.0 -25.0 0.986201 5 25.0 -25.0 25.0 0.994429 6 25.0 25.0 -25.0 0.990592 7 25.0 25.0 25.0 0.995944 REL: 8 0.859797 7.949685 0.993711 rel = 0.865239 Number of iterations 10 Min cost was 0.859797 Number of FunctionCalls 940 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 42.900652 sec Parameters at optimum (transmm) 0.47930 -0.55081 -1.75326 Parameters at optimum (rotdeg) 2.75156 0.27589 -0.41850 Final costs ---------------- Number of surface hits 239836 WM Intensity 1468.2504 +/- 504.8573 Ctx Intensity 1490.1894 +/- 532.9470 Pct Contrast 0.5808 +/- 25.7476 Cost 0.8598 RelCost 0.8956 Reg at min cost was 0.99999 -0.00092 -0.00521 -2.32046; 0.00448 -0.37481 0.92709 -25.45193; 0.00280 0.92710 0.37480 15.67993; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/003/register.dof6.dat, type = 14 Original Reg 0.99990 -0.00264 -0.01378 -2.70172; 0.01214 -0.32987 0.94395 -24.05591; 0.00704 0.94402 0.32981 18.59664; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00008 -0.00173 -0.00858 -0.38126; 0.00766 0.04494 0.01686 1.39602; 0.00424 0.01692 -0.04500 2.91671; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.583394 Computing change in rh position Surface-RMS-Diff-mm 2.681495 1.102509 5.323680 mri_segreg done MinCost: 0.859797 1468.250389 1490.189416 0.580772 tkregister2_cmdl --mov bold/003/template.nii.gz --reg bold/003/register.dof6.dat --noedit --ltaout bold/003/register.dof6.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/003/template.nii.gz reg file bold/003/register.dof6.dat LoadVol 0 ZeroCRAS 0 7.4.1 Diagnostic Level -1 ---- Input registration matrix -------- 0.99999 -0.00092 -0.00521 -2.32046; 0.00448 -0.37481 0.92709 -25.45193; 0.00280 0.92710 0.37480 15.67993; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: This is an unsigined short. INFO: loading target /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/003/template.nii.gz INFO: This is an unsigined short. Tmov: -------------------- -2.00000 0.00000 0.00000 110.00000; 0.00000 0.00000 2.00000 -64.00000; 0.00000 -2.00000 0.00000 110.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99999 -0.00092 -0.00521 -2.32046; 0.00448 -0.37481 0.92709 -25.45193; 0.00280 0.92710 0.37480 15.67993; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = 20231006_da047 RegMat --------------------------- 0.99999 -0.00092 -0.00521 -2.32046; 0.00448 -0.37481 0.92709 -25.45193; 0.00280 0.92710 0.37480 15.67993; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Wed Jun 18 10:07:36 EDT 2025 Ended at Wed Jun 18 10:08:56 EDT 2025 BBR-Run-Time-Sec 80 bbregister Done To check results, run: tkregisterfv --mov bold/003/template.nii.gz --reg bold/003/register.dof6.lta --surfs --sd /Volumes/umms-hillmera/asem_ptsd/DA047 Run: 004 ---------------- Wed Jun 18 10:08:56 EDT 2025 -------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 bbregister --s 20231006_da047 --init-coreg --6 --bold --mov bold/004/template.nii.gz --reg bold/004/register.dof6.dat --lta bold/004/register.dof6.lta --init-reg-out bold/004/init.register.dof6.dat tmp bold/004/tmp.bbregister.75703 Log file is bold/004/register.dof6.log Wed Jun 18 10:08:56 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 /Applications/freesurfer/bin/bbregister --s 20231006_da047 --init-coreg --6 --bold --mov bold/004/template.nii.gz --reg bold/004/register.dof6.dat --lta bold/004/register.dof6.lta --init-reg-out bold/004/init.register.dof6.dat FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 FREESURFER_HOME /Applications/freesurfer mri_convert bold/004/template.nii.gz bold/004/tmp.bbregister.75703/template.nii mri_convert bold/004/template.nii.gz bold/004/tmp.bbregister.75703/template.nii reading from bold/004/template.nii.gz... INFO: This is an unsigined short. TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) writing to bold/004/tmp.bbregister.75703/template.nii... mri_coreg --s 20231006_da047 --mov bold/004/tmp.bbregister.75703/template.nii --regdat bold/004/tmp.bbregister.75703/reg.init.dat --reg bold/004/tmp.bbregister.75703/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 cmdline mri_coreg --s 20231006_da047 --mov bold/004/tmp.bbregister.75703/template.nii --regdat bold/004/tmp.bbregister.75703/reg.init.dat --reg bold/004/tmp.bbregister.75703/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov bold/004/tmp.bbregister.75703/template.nii INFO: This is an unsigined short. Reading in ref /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/brainmask.mgz Reading in and applying refmask /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz Setting cras translation parameters to align volume centers Init matrix params 0.5000 4.0430 -1.8403 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 -0.50000; 0.00000 1.00000 0.00000 -4.04300; 0.00000 0.00000 1.00000 1.84027; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt 0.5000 4.0430 -1.8403 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 3890.0000 mov gstd 1.6917 1.6917 1.6917 Smoothing mov refsat = 115.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0336930723 nhits = 93515 out of 16777216, Percent Overlap: 35.7 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 0.50000; 0.00000 1.00000 0.00000 4.04300; 0.00000 0.00000 1.00000 -1.84027; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.50000 0.00000 0.00000 -9.25000; 0.00000 0.20017 -0.45818 87.39588; 0.00000 -0.45818 -0.20017 115.44038; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -3.50000 28.04300 -11.84027 0.00000 0.00000 0.00000 -1.0413427 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: -3.500000 28.042999 -11.840268 0.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0683954954 #@# 4 188 -3.50000 28.04300 -11.84027 0.00000 0.00000 0.00000 -1.0683955 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.068395 #@# 4 197 -3.49000 28.04300 -11.84027 0.00000 0.00000 0.00000 -1.0683964 #@# 4 200 -3.49000 26.42496 -11.84027 0.00000 0.00000 0.00000 -1.0691869 #@# 4 201 -3.49000 26.57273 -11.84027 0.00000 0.00000 0.00000 -1.0692042 #@# 4 207 -3.49000 26.56273 -11.84027 0.00000 0.00000 0.00000 -1.0692048 #@# 4 212 -3.49000 26.56273 -13.45830 0.00000 0.00000 0.00000 -1.0693055 #@# 4 213 -3.49000 26.56273 -12.72223 0.00000 0.00000 0.00000 -1.0696323 #@# 4 217 -3.49000 26.56273 -12.73223 0.00000 0.00000 0.00000 -1.0696324 #@# 4 223 -3.49000 26.56273 -12.73223 -0.61803 0.00000 0.00000 -1.0696738 #@# 4 225 -3.49000 26.56273 -12.73223 -0.39128 0.00000 0.00000 -1.0696869 #@# 4 230 -3.49000 26.56273 -12.73223 -0.40128 0.00000 0.00000 -1.0696870 #@# 4 235 -3.49000 26.56273 -12.73223 -0.40128 -0.61803 0.00000 -1.0697056 #@# 4 237 -3.49000 26.56273 -12.73223 -0.40128 -0.37309 0.00000 -1.0697317 #@# 4 241 -3.49000 26.56273 -12.73223 -0.40128 -0.38309 0.00000 -1.0697345 powell nthiter 1: fret = -1.069734 #@# 4 270 -3.49000 26.46375 -12.73223 -0.40128 -0.38309 0.00000 -1.0697390 #@# 4 275 -3.49000 26.45375 -12.73223 -0.40128 -0.38309 0.00000 -1.0697402 #@# 4 281 -3.49000 26.45375 -12.35026 -0.40128 -0.38309 0.00000 -1.0697405 #@# 4 282 -3.49000 26.45375 -12.54049 -0.40128 -0.38309 0.00000 -1.0697663 #@# 4 284 -3.49000 26.45375 -12.56049 -0.40128 -0.38309 0.00000 -1.0697672 #@# 4 294 -3.49000 26.45375 -12.56049 -0.56939 -0.38309 0.00000 -1.0697691 #@# 4 295 -3.49000 26.45375 -12.56049 -0.50178 -0.38309 0.00000 -1.0697709 #@# 4 296 -3.49000 26.45375 -12.56049 -0.49178 -0.38309 0.00000 -1.0697712 #@# 4 297 -3.49000 26.45375 -12.56049 -0.45721 -0.38309 0.00000 -1.0697765 Powell done niters total = 1 OptTimeSec 5.2 sec OptTimeMin 0.09 min nEvals 323 Final optimized parameters -3.49000001 26.45375061 -12.56048965 -0.45721269 -0.38308638 0.00000000 Final matrix parameters -3.4900 26.4538 -12.5605 -0.4572 -0.3831 -0.0100 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.069776518699294 --------------------------------- Final RefRAS-to-MovRAS 0.99998 0.00000 -0.00669 -3.49000; -0.00005 0.99997 -0.00798 26.45375; 0.00669 0.00798 0.99995 -12.56049; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.49999 -0.00334 0.00000 -6.82566; 0.00131 0.19651 -0.45976 79.77739; -0.00307 -0.45975 -0.19651 106.16846; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters -3.4900 26.4538 -12.5605 -0.4572 -0.3831 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters -3.4900 26.4538 -12.5605 -0.4572 -0.3831 0.0000 nhits = 91668 out of 16777216, Percent Overlap: 35.0 mri_coreg RunTimeSec 29.9 sec To check run: tkregisterfv --mov bold/004/tmp.bbregister.75703/template.nii --targ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/brainmask.mgz --reg bold/004/tmp.bbregister.75703/mri_coreg.lta --s 20231006_da047 --surfs mri_coreg done mri_segreg --mov bold/004/tmp.bbregister.75703/template.nii --init-reg bold/004/tmp.bbregister.75703/reg.init.dat --out-reg bold/004/tmp.bbregister.75703/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 mri_segreg --mov bold/004/tmp.bbregister.75703/template.nii --init-reg bold/004/tmp.bbregister.75703/reg.init.dat --out-reg bold/004/tmp.bbregister.75703/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/004/tmp.bbregister.75703/template.nii regfile bold/004/tmp.bbregister.75703/reg.init.dat subject 20231006_da047 dof 6 outregfile bold/004/tmp.bbregister.75703/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1751179857 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99998 -0.00000 -0.00669 -3.49001; 0.00615 -0.39302 0.91951 -20.45410; 0.00263 0.91953 0.39302 17.50256; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.986891 1 -25.0 -25.0 25.0 1.048177 2 -25.0 25.0 -25.0 1.017895 3 -25.0 25.0 25.0 0.982835 4 25.0 -25.0 -25.0 1.029632 5 25.0 -25.0 25.0 1.039532 6 25.0 25.0 -25.0 1.017304 7 25.0 25.0 25.0 1.049607 REL: 8 1.070162 8.171874 1.021484 rel = 1.04765 Initial costs ---------------- Number of surface hits 2399 WM Intensity 1609.5230 +/- 524.7613 Ctx Intensity 1556.7236 +/- 502.1012 Pct Contrast -3.3287 +/- 22.8622 Cost 1.0702 RelCost 1.0477 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0661 1.0661 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0497 1.0497 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0415 1.0415 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 1.0234 1.0234 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9935 0.9935 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.9582 0.9582 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.9067 0.9067 0.0 Brute Force -------------------------- Min cost was 0.906733 Number of iterations 729 Search time 0.792923 sec Parameters at best (transmm, rotdeg) 0.000 -4.000 0.000 -4.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -4 2 0 3 -4 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.906733 2 1.000 -4.000 0.000 -4.000 0.000 0.000 0.8877825829 6 0.618 -4.000 0.000 -4.000 0.000 0.000 0.8739348271 12 0.587 -4.000 0.000 -4.000 0.000 0.000 0.8739232311 13 0.601 -4.000 0.000 -4.000 0.000 0.000 0.8738842970 15 0.600 -4.000 0.000 -4.000 0.000 0.000 0.8738841725 24 0.600 -3.970 0.000 -4.000 0.000 0.000 0.8727038544 25 0.600 -3.858 0.000 -4.000 0.000 0.000 0.8714938495 27 0.600 -3.887 0.000 -4.000 0.000 0.000 0.8714392122 28 0.600 -3.878 0.000 -4.000 0.000 0.000 0.8714200410 29 0.600 -3.877 0.000 -4.000 0.000 0.000 0.8714195920 35 0.600 -3.877 -0.618 -4.000 0.000 0.000 0.8697017647 36 0.600 -3.877 -1.000 -4.000 0.000 0.000 0.8687285592 38 0.600 -3.877 -0.854 -4.000 0.000 0.000 0.8670160524 40 0.600 -3.877 -0.853 -4.000 0.000 0.000 0.8670149002 41 0.600 -3.877 -0.849 -4.000 0.000 0.000 0.8670140756 43 0.600 -3.877 -0.851 -4.000 0.000 0.000 0.8670137367 51 0.600 -3.877 -0.851 -4.260 0.000 0.000 0.8638254002 52 0.600 -3.877 -0.851 -4.262 0.000 0.000 0.8638229140 54 0.600 -3.877 -0.851 -4.269 0.000 0.000 0.8638221627 55 0.600 -3.877 -0.851 -4.266 0.000 0.000 0.8638179025 62 0.600 -3.877 -0.851 -4.266 -0.618 0.000 0.8596070308 64 0.600 -3.877 -0.851 -4.266 -0.387 0.000 0.8548081628 66 0.600 -3.877 -0.851 -4.266 -0.408 0.000 0.8547887789 67 0.600 -3.877 -0.851 -4.266 -0.401 0.000 0.8547815122 68 0.600 -3.877 -0.851 -4.266 -0.400 0.000 0.8547811384 69 0.600 -3.877 -0.851 -4.266 -0.399 0.000 0.8547806214 78 0.600 -3.877 -0.851 -4.266 -0.399 -0.028 0.8544593352 80 0.600 -3.877 -0.851 -4.266 -0.399 -0.066 0.8541480884 82 0.600 -3.877 -0.851 -4.266 -0.399 -0.082 0.8540971996 83 0.600 -3.877 -0.851 -4.266 -0.399 -0.085 0.8540927108 84 0.600 -3.877 -0.851 -4.266 -0.399 -0.089 0.8540884853 88 0.600 -3.877 -0.851 -4.266 -0.399 -0.090 0.8540877851 powell nthiter 1: fret = 0.854088 100 0.599 -3.877 -0.851 -4.266 -0.399 -0.090 0.8540872854 110 0.599 -3.845 -0.851 -4.266 -0.399 -0.090 0.8539621217 111 0.599 -3.850 -0.851 -4.266 -0.399 -0.090 0.8539229761 112 0.599 -3.857 -0.851 -4.266 -0.399 -0.090 0.8538843358 114 0.599 -3.859 -0.851 -4.266 -0.399 -0.090 0.8538802748 115 0.599 -3.860 -0.851 -4.266 -0.399 -0.090 0.8538798457 125 0.599 -3.860 -0.909 -4.266 -0.399 -0.090 0.8535961315 126 0.599 -3.860 -0.894 -4.266 -0.399 -0.090 0.8534895880 127 0.599 -3.860 -0.888 -4.266 -0.399 -0.090 0.8534864657 128 0.599 -3.860 -0.891 -4.266 -0.399 -0.090 0.8534845436 139 0.599 -3.860 -0.891 -4.270 -0.399 -0.090 0.8534315398 140 0.599 -3.860 -0.891 -4.295 -0.399 -0.090 0.8533557071 142 0.599 -3.860 -0.891 -4.288 -0.399 -0.090 0.8533401219 153 0.599 -3.860 -0.891 -4.288 -0.394 -0.090 0.8533328186 155 0.599 -3.860 -0.891 -4.288 -0.395 -0.090 0.8533311541 165 0.599 -3.860 -0.891 -4.288 -0.395 -0.082 0.8533281715 166 0.599 -3.860 -0.891 -4.288 -0.395 -0.085 0.8533275873 powell nthiter 2: fret = 0.853328 189 0.599 -3.830 -0.891 -4.288 -0.395 -0.085 0.8532631342 190 0.599 -3.839 -0.891 -4.288 -0.395 -0.085 0.8532304051 191 0.599 -3.841 -0.891 -4.288 -0.395 -0.085 0.8532289843 203 0.599 -3.841 -0.890 -4.288 -0.395 -0.085 0.8532286782 204 0.599 -3.841 -0.889 -4.288 -0.395 -0.085 0.8532286084 217 0.599 -3.841 -0.889 -4.303 -0.395 -0.085 0.8531792771 238 0.599 -3.841 -0.889 -4.303 -0.395 -0.079 0.8531777497 243 0.599 -3.822 -0.887 -4.318 -0.395 -0.074 0.8531703263 246 0.599 -3.792 -0.883 -4.343 -0.395 -0.065 0.8529808763 247 0.599 -3.743 -0.878 -4.383 -0.395 -0.051 0.8529318309 248 0.599 -3.760 -0.880 -4.369 -0.395 -0.056 0.8528814788 250 0.599 -3.772 -0.881 -4.359 -0.395 -0.059 0.8528745442 252 0.599 -3.768 -0.881 -4.363 -0.395 -0.058 0.8528670670 255 0.599 -3.768 -0.881 -4.363 -0.395 -0.058 0.8528670346 256 0.599 -3.768 -0.881 -4.363 -0.395 -0.058 0.8528667661 257 0.599 -3.768 -0.881 -4.362 -0.395 -0.058 0.8528667470 powell nthiter 3: fret = 0.852867 267 0.616 -3.768 -0.881 -4.362 -0.395 -0.058 0.8528029258 269 0.615 -3.768 -0.881 -4.362 -0.395 -0.058 0.8528026771 277 0.615 -3.768 -0.881 -4.362 -0.395 -0.047 0.8527888090 279 0.615 -3.768 -0.881 -4.362 -0.395 -0.042 0.8527874845 280 0.615 -3.768 -0.881 -4.362 -0.395 -0.043 0.8527874565 288 0.615 -3.768 -0.843 -4.362 -0.395 -0.043 0.8525595229 290 0.615 -3.768 -0.838 -4.362 -0.395 -0.043 0.8525555507 292 0.615 -3.768 -0.839 -4.362 -0.395 -0.043 0.8525550772 302 0.615 -3.768 -0.839 -4.396 -0.395 -0.043 0.8520675086 314 0.615 -3.768 -0.839 -4.396 -0.353 -0.043 0.8519482358 315 0.615 -3.768 -0.839 -4.396 -0.363 -0.043 0.8519258379 316 0.615 -3.768 -0.839 -4.396 -0.365 -0.043 0.8519253822 318 0.615 -3.768 -0.839 -4.396 -0.364 -0.043 0.8519250385 320 0.615 -3.749 -0.837 -4.411 -0.364 -0.038 0.8518018954 325 0.615 -3.747 -0.837 -4.413 -0.364 -0.037 0.8518005864 330 0.615 -3.747 -0.837 -4.413 -0.364 -0.037 0.8518005351 powell nthiter 4: fret = 0.851801 341 0.606 -3.747 -0.837 -4.413 -0.364 -0.037 0.8517824029 342 0.607 -3.747 -0.837 -4.413 -0.364 -0.037 0.8517820272 352 0.607 -3.747 -0.837 -4.413 -0.364 -0.024 0.8517747941 361 0.607 -3.747 -0.827 -4.413 -0.364 -0.024 0.8516879149 362 0.607 -3.747 -0.774 -4.413 -0.364 -0.024 0.8515801761 364 0.607 -3.747 -0.791 -4.413 -0.364 -0.024 0.8515417528 377 0.607 -3.747 -0.791 -4.418 -0.364 -0.024 0.8515234818 378 0.607 -3.747 -0.791 -4.419 -0.364 -0.024 0.8515224871 387 0.607 -3.747 -0.791 -4.419 -0.356 -0.024 0.8515157950 388 0.607 -3.747 -0.791 -4.419 -0.357 -0.024 0.8515156536 391 0.607 -3.728 -0.789 -4.435 -0.357 -0.019 0.8514881101 395 0.607 -3.735 -0.790 -4.429 -0.357 -0.021 0.8514567254 396 0.607 -3.736 -0.790 -4.428 -0.357 -0.021 0.8514561629 403 0.607 -3.736 -0.790 -4.428 -0.357 -0.021 0.8514561050 410 0.604 -3.732 -0.772 -4.434 -0.354 -0.015 0.8513831470 412 0.603 -3.731 -0.768 -4.435 -0.354 -0.014 0.8513791722 413 0.603 -3.731 -0.767 -4.436 -0.354 -0.014 0.8513788911 415 0.603 -3.731 -0.767 -4.436 -0.354 -0.013 0.8513788106 powell nthiter 5: fret = 0.851379 428 0.586 -3.731 -0.767 -4.436 -0.354 -0.013 0.8512543961 429 0.559 -3.731 -0.767 -4.436 -0.354 -0.013 0.8511476276 432 0.566 -3.731 -0.767 -4.436 -0.354 -0.013 0.8511377153 433 0.565 -3.731 -0.767 -4.436 -0.354 -0.013 0.8511377091 442 0.565 -3.731 -0.767 -4.436 -0.354 0.045 0.8508935237 443 0.565 -3.731 -0.767 -4.436 -0.354 0.034 0.8508354547 444 0.565 -3.731 -0.767 -4.436 -0.354 0.026 0.8508300171 445 0.565 -3.731 -0.767 -4.436 -0.354 0.029 0.8508280472 446 0.565 -3.731 -0.767 -4.436 -0.354 0.030 0.8508275131 453 0.565 -3.724 -0.766 -4.442 -0.354 0.032 0.8507989221 454 0.565 -3.724 -0.766 -4.441 -0.354 0.032 0.8507983798 455 0.565 -3.725 -0.766 -4.441 -0.354 0.031 0.8507973217 458 0.565 -3.725 -0.766 -4.441 -0.354 0.031 0.8507970110 460 0.565 -3.725 -0.766 -4.441 -0.354 0.031 0.8507967793 482 0.565 -3.725 -0.766 -4.441 -0.319 0.031 0.8506243873 484 0.565 -3.725 -0.766 -4.441 -0.323 0.031 0.8506226695 494 0.566 -3.727 -0.776 -4.437 -0.324 0.028 0.8506014218 495 0.566 -3.727 -0.775 -4.438 -0.324 0.028 0.8505998938 496 0.566 -3.727 -0.774 -4.438 -0.324 0.029 0.8505998740 498 0.566 -3.727 -0.774 -4.438 -0.324 0.029 0.8505997065 499 0.566 -3.727 -0.774 -4.438 -0.324 0.029 0.8505995037 powell nthiter 6: fret = 0.850600 509 0.563 -3.727 -0.774 -4.438 -0.324 0.029 0.8505845088 511 0.554 -3.727 -0.774 -4.438 -0.324 0.029 0.8505828065 512 0.558 -3.727 -0.774 -4.438 -0.324 0.029 0.8505741601 523 0.558 -3.727 -0.774 -4.438 -0.324 0.033 0.8505694821 524 0.558 -3.727 -0.774 -4.438 -0.324 0.034 0.8505693439 534 0.558 -3.729 -0.775 -4.436 -0.324 0.034 0.8505673058 535 0.558 -3.729 -0.775 -4.436 -0.324 0.035 0.8505668662 536 0.558 -3.729 -0.775 -4.436 -0.324 0.035 0.8505667879 539 0.558 -3.729 -0.775 -4.436 -0.324 0.035 0.8505667320 553 0.558 -3.729 -0.775 -4.438 -0.324 0.035 0.8505640072 564 0.558 -3.729 -0.775 -4.438 -0.323 0.035 0.8505600860 565 0.558 -3.729 -0.775 -4.438 -0.319 0.035 0.8505519711 577 0.559 -3.729 -0.777 -4.437 -0.320 0.034 0.8505516189 578 0.559 -3.729 -0.776 -4.438 -0.320 0.034 0.8505515188 579 0.559 -3.729 -0.776 -4.438 -0.320 0.034 0.8505514216 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 1.024085 1 -25.0 -25.0 25.0 1.022913 2 -25.0 25.0 -25.0 0.987766 3 -25.0 25.0 25.0 0.963116 4 25.0 -25.0 -25.0 0.998451 5 25.0 -25.0 25.0 1.021754 6 25.0 25.0 -25.0 1.003118 7 25.0 25.0 25.0 0.987489 REL: 8 0.850551 8.008692 1.001086 rel = 0.849628 Number of iterations 6 Min cost was 0.850551 Number of FunctionCalls 583 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.641180 sec Parameters at optimum (transmm) 0.55870 -3.72897 -0.77597 Parameters at optimum (rotdeg) -4.43755 -0.31998 0.03413 Final costs ---------------- Number of surface hits 2399 WM Intensity 1505.8462 +/- 486.7854 Ctx Intensity 1537.3013 +/- 516.9222 Pct Contrast 1.5990 +/- 21.8090 Cost 0.8506 RelCost 1.0477 Reg at min cost was 0.99995 -0.00510 -0.00904 -3.02620; 0.00693 -0.32070 0.94715 -22.76968; 0.00773 0.94717 0.32065 18.23691; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/004/tmp.bbregister.75703/bbr.pass1.dat, type = 14 Original Reg 0.99998 -0.00000 -0.00669 -3.49001; 0.00615 -0.39302 0.91951 -20.45410; 0.00263 0.91953 0.39302 17.50256; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00003 0.00510 0.00236 -0.46380; -0.00078 -0.07232 -0.02765 2.31558; -0.00510 -0.02764 0.07237 -0.73436; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 4.895412 Computing change in rh position Surface-RMS-Diff-mm 4.980636 2.520655 10.437375 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov bold/004/tmp.bbregister.75703/template.nii --init-reg bold/004/tmp.bbregister.75703/bbr.pass1.dat --out-reg bold/004/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/004/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/004/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/004/tmp.bbregister.75703/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 mri_segreg --mov bold/004/tmp.bbregister.75703/template.nii --init-reg bold/004/tmp.bbregister.75703/bbr.pass1.dat --out-reg bold/004/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/004/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/004/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/004/tmp.bbregister.75703/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/004/tmp.bbregister.75703/template.nii regfile bold/004/tmp.bbregister.75703/bbr.pass1.dat subject 20231006_da047 dof 6 outregfile bold/004/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750409711 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99995 -0.00510 -0.00904 -3.02620; 0.00693 -0.32070 0.94715 -22.76968; 0.00773 0.94717 0.32065 18.23691; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.999086 1 -25.0 -25.0 25.0 1.011014 2 -25.0 25.0 -25.0 0.995068 3 -25.0 25.0 25.0 0.986834 4 25.0 -25.0 -25.0 1.007484 5 25.0 -25.0 25.0 1.008420 6 25.0 25.0 -25.0 0.991791 7 25.0 25.0 25.0 1.002772 REL: 8 0.910979 8.002470 1.000309 rel = 0.910698 Initial costs ---------------- Number of surface hits 239836 WM Intensity 1512.5909 +/- 485.2781 Ctx Intensity 1532.4124 +/- 503.3010 Pct Contrast 0.8806 +/- 22.1957 Cost 0.9110 RelCost 0.9107 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.8615 0.8615 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.8604 0.8604 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.8602 0.8602 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.8590 0.8590 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.8585 0.8585 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.8584 0.8584 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.8575 0.8575 0.0 21 -0.1000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.8574 0.8574 0.0 22 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.0000 0.8561 0.8561 0.0 85 -0.1000 0.0000 -0.1000 -0.1000 0.0000 0.0000 0.8550 0.8550 0.0 94 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.8550 0.8550 0.0 112 -0.1000 0.0000 0.0000 -0.1000 0.0000 0.0000 0.8537 0.8537 0.0 309 0.0000 -0.1000 0.1000 0.0000 0.0000 -0.1000 0.8532 0.8532 0.0 334 0.0000 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.8527 0.8527 0.0 337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.8517 0.8517 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.8506 0.8506 0.0 Brute Force -------------------------- Min cost was 0.850551 Number of iterations 729 Search time 0.609110 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.910979 7 -0.087 0.000 0.000 0.000 0.000 0.000 0.9106722573 9 -0.083 0.000 0.000 0.000 0.000 0.000 0.9106720228 11 -0.085 0.000 0.000 0.000 0.000 0.000 0.9106718460 19 -0.085 0.002 0.000 0.000 0.000 0.000 0.9106660119 20 -0.085 0.094 0.000 0.000 0.000 0.000 0.9105745063 23 -0.085 0.095 0.000 0.000 0.000 0.000 0.9105738705 24 -0.085 0.137 0.000 0.000 0.000 0.000 0.9105704477 25 -0.085 0.119 0.000 0.000 0.000 0.000 0.9105649196 27 -0.085 0.121 0.000 0.000 0.000 0.000 0.9105648673 36 -0.085 0.121 -0.232 0.000 0.000 0.000 0.9099159886 37 -0.085 0.121 -0.231 0.000 0.000 0.000 0.9099154420 38 -0.085 0.121 -0.213 0.000 0.000 0.000 0.9099119533 40 -0.085 0.121 -0.217 0.000 0.000 0.000 0.9099118882 41 -0.085 0.121 -0.215 0.000 0.000 0.000 0.9099118136 44 -0.085 0.121 -0.215 1.000 0.000 0.000 0.9018601035 45 -0.085 0.121 -0.215 2.618 0.000 0.000 0.8978993408 46 -0.085 0.121 -0.215 2.381 0.000 0.000 0.8964899326 48 -0.085 0.121 -0.215 1.853 0.000 0.000 0.8960648604 50 -0.085 0.121 -0.215 2.021 0.000 0.000 0.8957009566 53 -0.085 0.121 -0.215 2.017 0.000 0.000 0.8957007059 54 -0.085 0.121 -0.215 2.018 0.000 0.000 0.8957006858 62 -0.085 0.121 -0.215 2.018 -0.064 0.000 0.8955194738 63 -0.085 0.121 -0.215 2.018 -0.116 0.000 0.8954895656 64 -0.085 0.121 -0.215 2.018 -0.105 0.000 0.8954856567 65 -0.085 0.121 -0.215 2.018 -0.102 0.000 0.8954854684 72 -0.085 0.121 -0.215 2.018 -0.102 -0.618 0.8945476712 74 -0.085 0.121 -0.215 2.018 -0.102 -0.385 0.8938810661 76 -0.085 0.121 -0.215 2.018 -0.102 -0.409 0.8938648554 78 -0.085 0.121 -0.215 2.018 -0.102 -0.448 0.8938576773 79 -0.085 0.121 -0.215 2.018 -0.102 -0.441 0.8938565921 80 -0.085 0.121 -0.215 2.018 -0.102 -0.437 0.8938561924 83 -0.085 0.121 -0.215 2.018 -0.102 -0.436 0.8938561879 powell nthiter 1: fret = 0.893856 91 0.297 0.121 -0.215 2.018 -0.102 -0.436 0.8907766975 93 0.269 0.121 -0.215 2.018 -0.102 -0.436 0.8907736465 94 0.280 0.121 -0.215 2.018 -0.102 -0.436 0.8907642806 95 0.282 0.121 -0.215 2.018 -0.102 -0.436 0.8907636622 102 0.282 -0.497 -0.215 2.018 -0.102 -0.436 0.8896073398 108 0.282 -0.495 -0.215 2.018 -0.102 -0.436 0.8896068774 109 0.282 -0.491 -0.215 2.018 -0.102 -0.436 0.8896060358 112 0.282 -0.490 -0.215 2.018 -0.102 -0.436 0.8896058164 113 0.282 -0.489 -0.215 2.018 -0.102 -0.436 0.8896057390 119 0.282 -0.489 -0.833 2.018 -0.102 -0.436 0.8833091362 120 0.282 -0.489 -1.215 2.018 -0.102 -0.436 0.8827648467 121 0.282 -0.489 -1.106 2.018 -0.102 -0.436 0.8826239175 123 0.282 -0.489 -1.119 2.018 -0.102 -0.436 0.8826201550 126 0.282 -0.489 -1.121 2.018 -0.102 -0.436 0.8826200707 134 0.282 -0.489 -1.122 2.400 -0.102 -0.436 0.8805225819 137 0.282 -0.489 -1.122 2.409 -0.102 -0.436 0.8805201881 138 0.282 -0.489 -1.122 2.413 -0.102 -0.436 0.8805198543 147 0.282 -0.489 -1.122 2.414 -0.057 -0.436 0.8804616636 150 0.282 -0.489 -1.122 2.414 -0.056 -0.436 0.8804616610 157 0.282 -0.489 -1.122 2.414 -0.056 -0.385 0.8803679976 158 0.282 -0.489 -1.122 2.414 -0.056 -0.327 0.8803214499 159 0.282 -0.489 -1.122 2.414 -0.056 -0.311 0.8803190665 161 0.282 -0.489 -1.122 2.414 -0.056 -0.317 0.8803188737 163 0.282 -0.489 -1.122 2.414 -0.056 -0.315 0.8803188714 165 0.649 -1.099 -2.028 2.809 -0.009 -0.194 0.8786063583 171 0.509 -0.866 -1.682 2.658 -0.027 -0.240 0.8776175060 172 0.534 -0.909 -1.745 2.686 -0.023 -0.232 0.8774261967 174 0.534 -0.908 -1.744 2.685 -0.023 -0.232 0.8774251786 176 0.532 -0.906 -1.740 2.684 -0.024 -0.232 0.8774246001 powell nthiter 2: fret = 0.877425 186 0.606 -0.906 -1.740 2.684 -0.024 -0.232 0.8773026618 187 0.596 -0.906 -1.740 2.684 -0.024 -0.232 0.8772902591 188 0.587 -0.906 -1.740 2.684 -0.024 -0.232 0.8772870258 197 0.586 -1.112 -1.740 2.684 -0.024 -0.232 0.8772145642 198 0.586 -1.032 -1.740 2.684 -0.024 -0.232 0.8771449864 199 0.586 -1.027 -1.740 2.684 -0.024 -0.232 0.8771392543 200 0.586 -0.981 -1.740 2.684 -0.024 -0.232 0.8771219038 201 0.586 -0.992 -1.740 2.684 -0.024 -0.232 0.8771187023 203 0.586 -0.991 -1.740 2.684 -0.024 -0.232 0.8771186373 205 0.586 -0.990 -1.740 2.684 -0.024 -0.232 0.8771186258 206 0.586 -0.989 -1.740 2.684 -0.024 -0.232 0.8771186060 214 0.586 -0.989 -1.740 2.684 -0.024 -0.249 0.8771078898 215 0.586 -0.989 -1.740 2.684 -0.024 -0.279 0.8770965828 217 0.586 -0.989 -1.740 2.684 -0.024 -0.296 0.8770940999 219 0.586 -0.989 -1.740 2.684 -0.024 -0.297 0.8770940304 220 0.586 -0.989 -1.740 2.684 -0.024 -0.298 0.8770939638 229 0.586 -0.989 -1.740 2.863 -0.024 -0.298 0.8767814822 230 0.586 -0.989 -1.740 2.861 -0.024 -0.298 0.8767802836 231 0.586 -0.989 -1.740 2.843 -0.024 -0.298 0.8767772428 234 0.586 -0.989 -1.740 2.841 -0.024 -0.298 0.8767770554 246 0.586 -0.989 -1.740 2.841 -0.015 -0.298 0.8767629510 247 0.586 -0.989 -1.740 2.841 0.017 -0.298 0.8767489542 249 0.586 -0.989 -1.740 2.841 0.007 -0.298 0.8767451896 250 0.586 -0.989 -1.740 2.841 0.006 -0.298 0.8767451309 259 0.583 -0.983 -1.732 2.837 0.006 -0.299 0.8767429280 261 0.584 -0.985 -1.734 2.838 0.006 -0.299 0.8767426450 powell nthiter 3: fret = 0.876743 272 0.619 -0.985 -1.734 2.838 0.006 -0.299 0.8767017575 273 0.621 -0.985 -1.734 2.838 0.006 -0.299 0.8767016970 282 0.621 -1.057 -1.734 2.838 0.006 -0.299 0.8765108126 283 0.621 -1.074 -1.734 2.838 0.006 -0.299 0.8765048864 284 0.621 -1.072 -1.734 2.838 0.006 -0.299 0.8765047735 285 0.621 -1.071 -1.734 2.838 0.006 -0.299 0.8765047702 293 0.621 -1.071 -1.734 2.838 0.006 -0.264 0.8764581453 295 0.621 -1.071 -1.734 2.838 0.006 -0.249 0.8764531255 298 0.621 -1.071 -1.734 2.838 0.006 -0.248 0.8764531207 320 0.621 -1.071 -1.734 2.838 0.011 -0.248 0.8764515519 321 0.621 -1.071 -1.734 2.838 0.013 -0.248 0.8764515377 322 0.621 -1.071 -1.734 2.838 0.014 -0.248 0.8764514178 332 0.606 -1.046 -1.696 2.822 0.012 -0.253 0.8763998764 334 0.607 -1.049 -1.701 2.824 0.012 -0.252 0.8763986559 336 0.608 -1.050 -1.702 2.824 0.012 -0.252 0.8763985139 337 0.609 -1.051 -1.704 2.825 0.012 -0.252 0.8763982391 340 0.608 -1.050 -1.703 2.825 0.012 -0.252 0.8763982349 341 0.633 -1.115 -1.672 2.811 0.019 -0.205 0.8763434716 348 0.630 -1.107 -1.676 2.813 0.018 -0.211 0.8763411481 350 0.631 -1.110 -1.675 2.812 0.018 -0.209 0.8763403839 354 0.631 -1.110 -1.675 2.812 0.018 -0.209 0.8763403602 355 0.631 -1.110 -1.675 2.812 0.018 -0.209 0.8763402949 powell nthiter 4: fret = 0.876340 363 0.695 -1.110 -1.675 2.812 0.018 -0.209 0.8763036082 364 0.674 -1.110 -1.675 2.812 0.018 -0.209 0.8762914753 366 0.675 -1.110 -1.675 2.812 0.018 -0.209 0.8762914166 369 0.676 -1.110 -1.675 2.812 0.018 -0.209 0.8762913904 376 0.660 -1.083 -1.635 2.795 0.016 -0.214 0.8762888976 377 0.667 -1.095 -1.653 2.803 0.017 -0.212 0.8762721885 378 0.668 -1.096 -1.654 2.803 0.017 -0.212 0.8762719614 380 0.669 -1.097 -1.656 2.804 0.017 -0.212 0.8762718544 392 0.669 -1.097 -1.656 2.804 0.017 -0.218 0.8762717765 394 0.669 -1.097 -1.656 2.804 0.017 -0.215 0.8762715507 396 0.669 -1.097 -1.656 2.804 0.017 -0.216 0.8762715502 406 0.669 -1.097 -1.656 2.821 0.017 -0.216 0.8762650201 416 0.669 -1.097 -1.656 2.822 0.019 -0.216 0.8762647808 417 0.669 -1.097 -1.656 2.822 0.023 -0.216 0.8762645098 425 0.678 -1.122 -1.644 2.817 0.025 -0.198 0.8762624175 426 0.674 -1.112 -1.649 2.819 0.024 -0.205 0.8762534358 428 0.674 -1.111 -1.649 2.819 0.024 -0.206 0.8762532568 powell nthiter 5: fret = 0.876253 440 0.671 -1.111 -1.649 2.819 0.024 -0.206 0.8762528739 450 0.667 -1.107 -1.643 2.817 0.023 -0.207 0.8762483193 451 0.666 -1.105 -1.641 2.816 0.023 -0.207 0.8762482070 453 0.667 -1.106 -1.642 2.816 0.023 -0.207 0.8762480880 463 0.667 -1.106 -1.642 2.816 0.023 -0.210 0.8762477453 479 0.667 -1.106 -1.642 2.817 0.023 -0.209 0.8762476301 488 0.667 -1.106 -1.642 2.817 0.035 -0.209 0.8762428662 490 0.667 -1.106 -1.642 2.817 0.036 -0.209 0.8762427881 491 0.667 -1.106 -1.642 2.817 0.037 -0.209 0.8762427249 500 0.669 -1.112 -1.639 2.816 0.038 -0.204 0.8762412462 502 0.668 -1.110 -1.640 2.817 0.038 -0.206 0.8762404480 503 0.668 -1.110 -1.640 2.817 0.038 -0.206 0.8762404432 504 0.668 -1.110 -1.640 2.817 0.038 -0.206 0.8762403954 511 0.663 -1.109 -1.630 2.813 0.052 -0.205 0.8762385113 powell nthiter 6: fret = 0.876240 529 0.663 -1.108 -1.636 2.815 0.038 -0.206 0.8762384741 530 0.662 -1.106 -1.634 2.814 0.038 -0.206 0.8762381439 553 0.662 -1.107 -1.635 2.831 0.038 -0.206 0.8762376524 556 0.662 -1.107 -1.635 2.832 0.038 -0.206 0.8762376454 557 0.662 -1.107 -1.635 2.833 0.038 -0.206 0.8762375892 558 0.662 -1.107 -1.635 2.835 0.038 -0.206 0.8762375209 576 0.671 -1.132 -1.623 2.830 0.040 -0.188 0.8762178011 578 0.670 -1.127 -1.625 2.831 0.040 -0.192 0.8762136730 579 0.669 -1.124 -1.627 2.832 0.039 -0.194 0.8762132764 580 0.669 -1.125 -1.626 2.832 0.039 -0.193 0.8762131163 583 0.669 -1.125 -1.626 2.832 0.039 -0.193 0.8762131148 585 0.670 -1.140 -1.613 2.847 0.041 -0.181 0.8761822305 588 0.671 -1.164 -1.592 2.871 0.043 -0.161 0.8761599013 589 0.671 -1.167 -1.588 2.875 0.044 -0.158 0.8761555916 590 0.671 -1.173 -1.583 2.881 0.044 -0.153 0.8761480807 591 0.671 -1.183 -1.574 2.891 0.045 -0.145 0.8761305833 592 0.672 -1.199 -1.560 2.907 0.047 -0.132 0.8760962424 593 0.673 -1.224 -1.537 2.934 0.049 -0.111 0.8760736632 596 0.673 -1.214 -1.546 2.924 0.048 -0.119 0.8760735543 598 0.673 -1.219 -1.542 2.928 0.049 -0.115 0.8760721578 602 0.673 -1.219 -1.542 2.928 0.049 -0.115 0.8760721460 604 0.673 -1.219 -1.542 2.928 0.049 -0.115 0.8760721343 powell nthiter 7: fret = 0.876072 613 0.738 -1.219 -1.542 2.928 0.049 -0.115 0.8760592712 614 0.710 -1.219 -1.542 2.928 0.049 -0.115 0.8760471021 617 0.704 -1.219 -1.542 2.928 0.049 -0.115 0.8760461240 618 0.702 -1.219 -1.542 2.928 0.049 -0.115 0.8760460148 620 0.703 -1.219 -1.542 2.928 0.049 -0.115 0.8760459798 631 0.700 -1.215 -1.537 2.926 0.049 -0.116 0.8760457560 632 0.701 -1.217 -1.539 2.927 0.049 -0.115 0.8760456985 634 0.701 -1.216 -1.538 2.926 0.049 -0.116 0.8760456833 643 0.701 -1.216 -1.538 2.926 0.049 -0.161 0.8759970623 644 0.701 -1.216 -1.538 2.926 0.049 -0.169 0.8759957985 660 0.701 -1.216 -1.538 2.941 0.049 -0.171 0.8759890353 663 0.701 -1.216 -1.538 2.942 0.049 -0.171 0.8759890241 672 0.701 -1.216 -1.538 2.942 0.124 -0.171 0.8758109937 674 0.701 -1.216 -1.538 2.942 0.135 -0.171 0.8758093865 675 0.701 -1.216 -1.538 2.942 0.132 -0.171 0.8758092192 679 0.702 -1.231 -1.525 2.957 0.134 -0.159 0.8757771668 680 0.703 -1.255 -1.504 2.981 0.136 -0.139 0.8757594367 681 0.703 -1.253 -1.505 2.979 0.136 -0.140 0.8757584519 684 0.702 -1.250 -1.508 2.976 0.136 -0.143 0.8757573397 685 0.702 -1.249 -1.508 2.976 0.136 -0.143 0.8757572902 686 0.702 -1.248 -1.509 2.975 0.135 -0.144 0.8757572659 688 0.702 -1.249 -1.509 2.975 0.135 -0.144 0.8757570826 powell nthiter 8: fret = 0.875757 700 0.705 -1.249 -1.509 2.975 0.135 -0.144 0.8757569398 703 0.704 -1.249 -1.509 2.975 0.135 -0.144 0.8757568774 712 0.705 -1.251 -1.512 2.977 0.136 -0.143 0.8757565305 713 0.705 -1.251 -1.512 2.976 0.136 -0.143 0.8757564453 723 0.705 -1.251 -1.512 2.976 0.136 -0.124 0.8757423981 724 0.705 -1.251 -1.512 2.976 0.136 -0.122 0.8757423351 750 0.705 -1.242 -1.520 2.967 0.135 -0.130 0.8757416859 752 0.705 -1.245 -1.516 2.971 0.135 -0.127 0.8757399608 753 0.705 -1.246 -1.516 2.971 0.135 -0.126 0.8757399464 754 0.705 -1.246 -1.516 2.971 0.135 -0.126 0.8757399005 755 0.705 -1.246 -1.516 2.971 0.135 -0.126 0.8757398976 756 0.705 -1.246 -1.516 2.971 0.135 -0.126 0.8757398415 765 0.706 -1.244 -1.519 2.969 0.135 -0.120 0.8757384421 768 0.706 -1.244 -1.520 2.969 0.135 -0.119 0.8757383331 powell nthiter 9: fret = 0.875738 784 0.715 -1.244 -1.520 2.969 0.135 -0.119 0.8757377214 785 0.712 -1.244 -1.520 2.969 0.135 -0.119 0.8757363526 786 0.711 -1.244 -1.520 2.969 0.135 -0.119 0.8757363346 804 0.711 -1.241 -1.522 2.966 0.135 -0.121 0.8757361535 805 0.711 -1.242 -1.521 2.967 0.135 -0.120 0.8757360032 806 0.711 -1.242 -1.521 2.967 0.135 -0.120 0.8757359418 821 0.711 -1.242 -1.521 2.972 0.135 -0.120 0.8757357947 822 0.711 -1.242 -1.521 2.970 0.135 -0.120 0.8757356684 832 0.711 -1.242 -1.521 2.970 0.133 -0.120 0.8757353781 850 0.711 -1.242 -1.521 2.970 0.131 -0.120 0.8757353772 852 0.711 -1.242 -1.521 2.970 0.131 -0.120 0.8757353517 854 0.711 -1.242 -1.521 2.970 0.131 -0.120 0.8757353508 powell nthiter 10: fret = 0.875735 866 0.712 -1.242 -1.521 2.970 0.131 -0.120 0.8757352360 885 0.712 -1.242 -1.521 2.970 0.131 -0.120 0.8757351803 890 0.712 -1.242 -1.521 2.970 0.131 -0.120 0.8757351691 926 0.712 -1.242 -1.521 2.970 0.131 -0.120 0.8757351352 powell nthiter 11: fret = 0.875735 Powell done niters = 11 Computing relative cost 0 -25.0 -25.0 -25.0 1.000358 1 -25.0 -25.0 25.0 1.023520 2 -25.0 25.0 -25.0 0.978270 3 -25.0 25.0 25.0 0.986734 4 25.0 -25.0 -25.0 0.994640 5 25.0 -25.0 25.0 0.993496 6 25.0 25.0 -25.0 0.993741 7 25.0 25.0 25.0 1.007898 REL: 8 0.875735 7.978658 0.997332 rel = 0.878078 Number of iterations 11 Min cost was 0.875735 Number of FunctionCalls 1002 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 45.211781 sec Parameters at optimum (transmm) 0.71178 -1.24206 -1.52138 Parameters at optimum (rotdeg) 2.97006 0.13075 -0.11973 Final costs ---------------- Number of surface hits 239836 WM Intensity 1484.8331 +/- 510.7978 Ctx Intensity 1502.5222 +/- 534.7078 Pct Contrast 0.3654 +/- 25.4294 Cost 0.8757 RelCost 0.9107 Reg at min cost was 0.99997 -0.00375 -0.00626 -2.32503; 0.00443 -0.36934 0.92928 -24.91979; 0.00580 0.92929 0.36931 15.51811; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/004/register.dof6.dat, type = 14 Original Reg 0.99995 -0.00510 -0.00904 -3.02620; 0.00693 -0.32070 0.94715 -22.76968; 0.00773 0.94717 0.32065 18.23691; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00003 -0.00135 -0.00278 -0.70117; 0.00250 0.04864 0.01787 2.15011; 0.00193 0.01788 -0.04866 2.71880; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.764542 Computing change in rh position Surface-RMS-Diff-mm 2.796768 1.233341 5.997557 mri_segreg done MinCost: 0.875735 1484.833076 1502.522215 0.365396 tkregister2_cmdl --mov bold/004/template.nii.gz --reg bold/004/register.dof6.dat --noedit --ltaout bold/004/register.dof6.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/004/template.nii.gz reg file bold/004/register.dof6.dat LoadVol 0 ZeroCRAS 0 7.4.1 Diagnostic Level -1 ---- Input registration matrix -------- 0.99997 -0.00375 -0.00626 -2.32503; 0.00443 -0.36934 0.92928 -24.91979; 0.00580 0.92929 0.36931 15.51811; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: This is an unsigined short. INFO: loading target /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/004/template.nii.gz INFO: This is an unsigined short. Tmov: -------------------- -2.00000 0.00000 0.00000 110.00000; 0.00000 0.00000 2.00000 -64.00000; 0.00000 -2.00000 0.00000 110.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99997 -0.00375 -0.00626 -2.32503; 0.00443 -0.36934 0.92928 -24.91979; 0.00580 0.92929 0.36931 15.51811; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = 20231006_da047 RegMat --------------------------- 0.99997 -0.00375 -0.00626 -2.32503; 0.00443 -0.36934 0.92928 -24.91979; 0.00580 0.92929 0.36931 15.51811; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Wed Jun 18 10:08:56 EDT 2025 Ended at Wed Jun 18 10:10:18 EDT 2025 BBR-Run-Time-Sec 82 bbregister Done To check results, run: tkregisterfv --mov bold/004/template.nii.gz --reg bold/004/register.dof6.lta --surfs --sd /Volumes/umms-hillmera/asem_ptsd/DA047 Run: 005 ---------------- Wed Jun 18 10:10:19 EDT 2025 -------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 bbregister --s 20231006_da047 --init-coreg --6 --bold --mov bold/005/template.nii.gz --reg bold/005/register.dof6.dat --lta bold/005/register.dof6.lta --init-reg-out bold/005/init.register.dof6.dat tmp bold/005/tmp.bbregister.75830 Log file is bold/005/register.dof6.log Wed Jun 18 10:10:19 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 /Applications/freesurfer/bin/bbregister --s 20231006_da047 --init-coreg --6 --bold --mov bold/005/template.nii.gz --reg bold/005/register.dof6.dat --lta bold/005/register.dof6.lta --init-reg-out bold/005/init.register.dof6.dat FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 FREESURFER_HOME /Applications/freesurfer mri_convert bold/005/template.nii.gz bold/005/tmp.bbregister.75830/template.nii mri_convert bold/005/template.nii.gz bold/005/tmp.bbregister.75830/template.nii reading from bold/005/template.nii.gz... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) writing to bold/005/tmp.bbregister.75830/template.nii... mri_coreg --s 20231006_da047 --mov bold/005/tmp.bbregister.75830/template.nii --regdat bold/005/tmp.bbregister.75830/reg.init.dat --reg bold/005/tmp.bbregister.75830/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 cmdline mri_coreg --s 20231006_da047 --mov bold/005/tmp.bbregister.75830/template.nii --regdat bold/005/tmp.bbregister.75830/reg.init.dat --reg bold/005/tmp.bbregister.75830/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov bold/005/tmp.bbregister.75830/template.nii INFO: This is an unsigined short. Reading in ref /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/brainmask.mgz Reading in and applying refmask /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz Setting cras translation parameters to align volume centers Init matrix params 0.5000 4.0430 1.1597 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 -0.50000; 0.00000 1.00000 0.00000 -4.04302; 0.00000 0.00000 1.00000 -1.15972; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt 0.5000 4.0430 1.1597 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 19951.0000 mov gstd 1.6917 1.6917 1.6917 Smoothing mov refsat = 115.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0312158859 nhits = 87541 out of 16777216, Percent Overlap: 33.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 0.50000; 0.00000 1.00000 0.00000 4.04302; 0.00000 0.00000 1.00000 1.15972; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.50000 0.00000 0.00000 -9.25000; 0.00000 0.20017 -0.45818 87.39588; 0.00000 -0.45818 -0.20017 113.44038; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -3.50000 32.04302 -10.84028 0.00000 0.00000 0.00000 -1.0440328 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: -3.500000 32.043022 -10.840283 0.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0696052313 #@# 4 188 -3.50000 32.04302 -10.84028 0.00000 0.00000 0.00000 -1.0696052 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.069605 #@# 4 195 -3.64615 32.04302 -10.84028 0.00000 0.00000 0.00000 -1.0696093 #@# 4 196 -3.61838 32.04302 -10.84028 0.00000 0.00000 0.00000 -1.0696100 #@# 4 197 -3.60376 32.04302 -10.84028 0.00000 0.00000 0.00000 -1.0696102 #@# 4 202 -3.60376 30.42499 -10.84028 0.00000 0.00000 0.00000 -1.0726228 #@# 4 205 -3.60376 26.46124 -10.84028 0.00000 0.00000 0.00000 -1.0746317 #@# 4 207 -3.60376 27.69736 -10.84028 0.00000 0.00000 0.00000 -1.0752970 #@# 4 208 -3.60376 27.78170 -10.84028 0.00000 0.00000 0.00000 -1.0753030 #@# 4 209 -3.60376 27.83934 -10.84028 0.00000 0.00000 0.00000 -1.0753042 #@# 4 215 -3.60376 27.82934 -12.45832 0.00000 0.00000 0.00000 -1.0762651 #@# 4 216 -3.60376 27.82934 -12.35708 0.00000 0.00000 0.00000 -1.0762866 #@# 4 219 -3.60376 27.82934 -12.13578 0.00000 0.00000 0.00000 -1.0762876 #@# 4 220 -3.60376 27.82934 -12.24074 0.00000 0.00000 0.00000 -1.0762918 #@# 4 221 -3.60376 27.82934 -12.23074 0.00000 0.00000 0.00000 -1.0762924 #@# 4 223 -3.60376 27.82934 -12.22074 0.00000 0.00000 0.00000 -1.0762929 #@# 4 226 -3.60376 27.82934 -12.22074 -1.61803 0.00000 0.00000 -1.0771961 #@# 4 231 -3.60376 27.82934 -12.22074 -1.71431 0.00000 0.00000 -1.0771998 #@# 4 232 -3.60376 27.82934 -12.22074 -1.70431 0.00000 0.00000 -1.0772034 #@# 4 239 -3.60376 27.82934 -12.22074 -1.70431 -0.61803 0.00000 -1.0772322 #@# 4 241 -3.60376 27.82934 -12.22074 -1.70431 -0.46862 0.00000 -1.0772443 #@# 4 242 -3.60376 27.82934 -12.22074 -1.70431 -0.39496 0.00000 -1.0772455 #@# 4 253 -3.60376 27.82934 -12.22074 -1.70431 -0.39496 0.38197 -1.0773159 #@# 4 254 -3.60376 27.82934 -12.22074 -1.70431 -0.39496 0.39232 -1.0773162 #@# 4 256 -3.60376 27.82934 -12.22074 -1.70431 -0.39496 0.40232 -1.0773175 powell nthiter 1: fret = -1.077317 #@# 4 264 -3.49224 27.82934 -12.22074 -1.70431 -0.39496 0.40232 -1.0773230 #@# 4 265 -3.51223 27.82934 -12.22074 -1.70431 -0.39496 0.40232 -1.0773242 #@# 4 271 -3.51223 27.21130 -12.22074 -1.70431 -0.39496 0.40232 -1.0774543 #@# 4 273 -3.51223 27.32122 -12.22074 -1.70431 -0.39496 0.40232 -1.0774592 #@# 4 274 -3.51223 27.30619 -12.22074 -1.70431 -0.39496 0.40232 -1.0774608 #@# 4 275 -3.51223 27.28056 -12.22074 -1.70431 -0.39496 0.40232 -1.0774616 #@# 4 282 -3.51223 27.29056 -11.83877 -1.70431 -0.39496 0.40232 -1.0775713 #@# 4 287 -3.51223 27.29056 -11.86006 -1.70431 -0.39496 0.40232 -1.0775728 #@# 4 294 -3.51223 27.29056 -11.86006 -2.32235 -0.39496 0.40232 -1.0776588 #@# 4 305 -3.51223 27.29056 -11.86006 -2.32235 -0.56657 0.40232 -1.0776638 #@# 4 308 -3.51223 27.29056 -11.86006 -2.32235 -0.63171 0.40232 -1.0776662 #@# 4 319 -3.51223 27.29056 -11.86006 -2.32235 -0.63171 0.50277 -1.0776752 powell nthiter 2: fret = -1.077675 #@# 4 329 -3.41860 27.29056 -11.86006 -2.32235 -0.63171 0.50277 -1.0776873 #@# 4 338 -3.41860 27.28056 -11.86006 -2.32235 -0.63171 0.50277 -1.0776875 #@# 4 345 -3.41860 27.28056 -11.47810 -2.32235 -0.63171 0.50277 -1.0777360 #@# 4 346 -3.41860 27.28056 -11.56664 -2.32235 -0.63171 0.50277 -1.0777384 #@# 4 347 -3.41860 27.28056 -11.54803 -2.32235 -0.63171 0.50277 -1.0777416 #@# 4 349 -3.41860 27.28056 -11.53803 -2.32235 -0.63171 0.50277 -1.0777434 #@# 4 356 -3.41860 27.28056 -11.53803 -2.57415 -0.63171 0.50277 -1.0777559 #@# 4 357 -3.41860 27.28056 -11.53803 -2.55180 -0.63171 0.50277 -1.0777591 #@# 4 358 -3.41860 27.28056 -11.53803 -2.47768 -0.63171 0.50277 -1.0777611 #@# 4 363 -3.41860 27.28056 -11.53803 -2.46768 -0.63171 0.50277 -1.0777613 #@# 4 379 -3.41860 27.28056 -11.53803 -2.46768 -0.63171 0.60071 -1.0777723 #@# 4 380 -3.41860 27.28056 -11.53803 -2.46768 -0.63171 0.62625 -1.0777731 #@# 4 382 -3.41860 27.28056 -11.53803 -2.46768 -0.63171 0.61625 -1.0777732 Powell done niters total = 2 OptTimeSec 7.7 sec OptTimeMin 0.13 min nEvals 382 Final optimized parameters -3.41859961 27.28055954 -11.53802872 -2.46768188 -0.63170677 0.61625326 Final matrix parameters -3.4186 27.2806 -11.5380 -2.4677 -0.6317 0.6163 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.077773239238025 --------------------------------- Final RefRAS-to-MovRAS 0.99988 0.01075 -0.01103 -3.41860; -0.01122 0.99901 -0.04305 27.28056; 0.01055 0.04317 0.99901 -11.53803; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.49994 -0.00551 -0.00538 -5.88919; -0.00303 0.18025 -0.46637 83.27668; -0.00708 -0.46635 -0.18020 102.36513; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters -3.4186 27.2806 -11.5380 -2.4677 -0.6317 0.6163 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters -3.4186 27.2806 -11.5380 -2.4677 -0.6317 0.6163 nhits = 85995 out of 16777216, Percent Overlap: 32.8 mri_coreg RunTimeSec 32.5 sec To check run: tkregisterfv --mov bold/005/tmp.bbregister.75830/template.nii --targ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/brainmask.mgz --reg bold/005/tmp.bbregister.75830/mri_coreg.lta --s 20231006_da047 --surfs mri_coreg done mri_segreg --mov bold/005/tmp.bbregister.75830/template.nii --init-reg bold/005/tmp.bbregister.75830/reg.init.dat --out-reg bold/005/tmp.bbregister.75830/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 mri_segreg --mov bold/005/tmp.bbregister.75830/template.nii --init-reg bold/005/tmp.bbregister.75830/reg.init.dat --out-reg bold/005/tmp.bbregister.75830/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/005/tmp.bbregister.75830/template.nii regfile bold/005/tmp.bbregister.75830/reg.init.dat subject 20231006_da047 dof 6 outregfile bold/005/tmp.bbregister.75830/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750600583 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99988 0.01075 -0.01103 -3.41860; 0.01416 -0.36039 0.93269 -22.59723; -0.00606 0.93274 0.36050 17.46851; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.047629 1 -25.0 -25.0 25.0 1.032559 2 -25.0 25.0 -25.0 1.000982 3 -25.0 25.0 25.0 1.000336 4 25.0 -25.0 -25.0 1.022902 5 25.0 -25.0 25.0 1.010556 6 25.0 25.0 -25.0 1.049874 7 25.0 25.0 25.0 1.020142 REL: 8 0.572623 8.184980 1.023122 rel = 0.559682 Initial costs ---------------- Number of surface hits 2399 WM Intensity 9712.7156 +/- 1114.6302 Ctx Intensity 10088.6624 +/- 1471.3699 Pct Contrast 3.1593 +/- 15.0141 Cost 0.5726 RelCost 0.5597 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0695 1.0695 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0668 1.0668 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 1.0138 1.0138 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9497 0.9497 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8861 0.8861 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8848 0.8848 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8746 0.8746 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.8321 0.8321 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8204 0.8204 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.7950 0.7950 0.0 337 0.0000 0.0000 -4.0000 0.0000 0.0000 0.0000 0.7900 0.7900 0.0 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.7328 0.7328 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5726 0.5726 0.0 Brute Force -------------------------- Min cost was 0.572623 Number of iterations 729 Search time 0.612918 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.572623 8 0.018 0.000 0.000 0.000 0.000 0.000 0.5724417192 9 0.035 0.000 0.000 0.000 0.000 0.000 0.5723673793 10 0.038 0.000 0.000 0.000 0.000 0.000 0.5723638882 11 0.040 0.000 0.000 0.000 0.000 0.000 0.5723620909 14 0.043 0.000 0.000 0.000 0.000 0.000 0.5723610212 15 0.042 0.000 0.000 0.000 0.000 0.000 0.5723607468 19 0.042 -1.618 0.000 0.000 0.000 0.000 0.5446894684 20 0.042 -0.994 0.000 0.000 0.000 0.000 0.5338753537 25 0.042 -1.014 0.000 0.000 0.000 0.000 0.5338371043 27 0.042 -1.009 0.000 0.000 0.000 0.000 0.5338305942 28 0.042 -1.008 0.000 0.000 0.000 0.000 0.5338305545 32 0.042 -1.008 -1.618 0.000 0.000 0.000 0.4828248263 33 0.042 -1.008 -1.164 0.000 0.000 0.000 0.4677968585 37 0.042 -1.008 -0.999 0.000 0.000 0.000 0.4660876461 38 0.042 -1.008 -0.979 0.000 0.000 0.000 0.4657708053 39 0.042 -1.008 -0.880 0.000 0.000 0.000 0.4652325889 40 0.042 -1.008 -0.899 0.000 0.000 0.000 0.4650809590 41 0.042 -1.008 -0.913 0.000 0.000 0.000 0.4650647996 42 0.042 -1.008 -0.909 0.000 0.000 0.000 0.4650607322 43 0.042 -1.008 -0.908 0.000 0.000 0.000 0.4650604286 44 0.042 -1.008 -0.907 0.000 0.000 0.000 0.4650598094 46 0.042 -1.008 -0.906 0.000 0.000 0.000 0.4650594283 48 0.042 -1.008 -0.906 1.000 0.000 0.000 0.4482212902 52 0.042 -1.008 -0.906 0.618 0.000 0.000 0.4453954503 58 0.042 -1.008 -0.906 0.624 0.000 0.000 0.4453933933 68 0.042 -1.008 -0.906 0.624 0.158 0.000 0.4424761536 69 0.042 -1.008 -0.906 0.624 0.175 0.000 0.4424403981 71 0.042 -1.008 -0.906 0.624 0.173 0.000 0.4424391356 81 0.042 -1.008 -0.906 0.624 0.173 -0.251 0.4420567429 82 0.042 -1.008 -0.906 0.624 0.173 -0.171 0.4415322511 83 0.042 -1.008 -0.906 0.624 0.173 -0.142 0.4413786792 84 0.042 -1.008 -0.906 0.624 0.173 -0.088 0.4413222288 85 0.042 -1.008 -0.906 0.624 0.173 -0.104 0.4412565592 87 0.042 -1.008 -0.906 0.624 0.173 -0.106 0.4412558397 powell nthiter 1: fret = 0.441256 97 0.052 -1.008 -0.906 0.624 0.173 -0.106 0.4412281404 98 0.061 -1.008 -0.906 0.624 0.173 -0.106 0.4412268313 99 0.057 -1.008 -0.906 0.624 0.173 -0.106 0.4412249938 100 0.058 -1.008 -0.906 0.624 0.173 -0.106 0.4412249210 108 0.058 -1.203 -0.906 0.624 0.173 -0.106 0.4409714066 109 0.058 -1.122 -0.906 0.624 0.173 -0.106 0.4408172614 110 0.058 -1.129 -0.906 0.624 0.173 -0.106 0.4407876708 111 0.058 -1.151 -0.906 0.624 0.173 -0.106 0.4407244548 113 0.058 -1.149 -0.906 0.624 0.173 -0.106 0.4407234288 114 0.058 -1.148 -0.906 0.624 0.173 -0.106 0.4407220012 117 0.058 -1.147 -0.906 0.624 0.173 -0.106 0.4407213883 122 0.058 -1.147 -1.524 0.624 0.173 -0.106 0.4399351699 124 0.058 -1.147 -1.226 0.624 0.173 -0.106 0.4342397599 125 0.058 -1.147 -1.225 0.624 0.173 -0.106 0.4342359987 126 0.058 -1.147 -1.190 0.624 0.173 -0.106 0.4341848023 128 0.058 -1.147 -1.196 0.624 0.173 -0.106 0.4341830026 130 0.058 -1.147 -1.197 0.624 0.173 -0.106 0.4341828802 139 0.058 -1.147 -1.197 1.006 0.173 -0.106 0.4341584727 140 0.058 -1.147 -1.197 0.816 0.173 -0.106 0.4327577217 141 0.058 -1.147 -1.197 0.817 0.173 -0.106 0.4327495284 142 0.058 -1.147 -1.197 0.867 0.173 -0.106 0.4325072733 144 0.058 -1.147 -1.197 0.870 0.173 -0.106 0.4325038996 154 0.058 -1.147 -1.197 0.870 0.151 -0.106 0.4323122280 156 0.058 -1.147 -1.197 0.870 0.103 -0.106 0.4321784604 157 0.058 -1.147 -1.197 0.870 0.110 -0.106 0.4321712379 159 0.058 -1.147 -1.197 0.870 0.109 -0.106 0.4321702751 169 0.058 -1.147 -1.197 0.870 0.109 -0.136 0.4321401775 170 0.058 -1.147 -1.197 0.870 0.109 -0.132 0.4321299019 171 0.058 -1.147 -1.197 0.870 0.109 -0.125 0.4321165368 173 0.058 -1.147 -1.197 0.870 0.109 -0.124 0.4321152910 174 0.058 -1.147 -1.197 0.870 0.109 -0.123 0.4321143293 175 0.058 -1.147 -1.197 0.870 0.109 -0.121 0.4321130941 powell nthiter 2: fret = 0.432113 186 0.006 -1.147 -1.197 0.870 0.109 -0.121 0.4314722196 188 -0.024 -1.147 -1.197 0.870 0.109 -0.121 0.4312997248 198 -0.024 -1.237 -1.197 0.870 0.109 -0.121 0.4284143875 200 -0.024 -1.307 -1.197 0.870 0.109 -0.121 0.4277971135 201 -0.024 -1.305 -1.197 0.870 0.109 -0.121 0.4277967590 210 -0.024 -1.305 -1.233 0.870 0.109 -0.121 0.4275530373 211 -0.024 -1.305 -1.238 0.870 0.109 -0.121 0.4275416640 212 -0.024 -1.305 -1.245 0.870 0.109 -0.121 0.4275400150 214 -0.024 -1.305 -1.242 0.870 0.109 -0.121 0.4275380904 224 -0.024 -1.305 -1.242 0.851 0.109 -0.121 0.4274966456 225 -0.024 -1.305 -1.242 0.849 0.109 -0.121 0.4274952286 228 -0.024 -1.305 -1.242 0.846 0.109 -0.121 0.4274923083 240 -0.024 -1.305 -1.242 0.846 0.110 -0.121 0.4274903765 241 -0.024 -1.305 -1.242 0.846 0.120 -0.121 0.4274891870 243 -0.024 -1.305 -1.242 0.846 0.116 -0.121 0.4274870917 244 -0.024 -1.305 -1.242 0.846 0.115 -0.121 0.4274866217 253 -0.024 -1.305 -1.242 0.846 0.115 -0.185 0.4273083379 254 -0.024 -1.305 -1.242 0.846 0.115 -0.184 0.4273075938 255 -0.024 -1.305 -1.242 0.846 0.115 -0.177 0.4273036678 258 -0.024 -1.305 -1.242 0.846 0.115 -0.170 0.4273036049 259 -0.024 -1.305 -1.242 0.846 0.115 -0.174 0.4273027436 260 -0.024 -1.305 -1.242 0.846 0.115 -0.175 0.4273027408 powell nthiter 3: fret = 0.427303 270 0.008 -1.305 -1.242 0.846 0.115 -0.175 0.4271780100 271 0.009 -1.305 -1.242 0.846 0.115 -0.175 0.4271758248 272 0.021 -1.305 -1.242 0.846 0.115 -0.175 0.4271745304 273 0.015 -1.305 -1.242 0.846 0.115 -0.175 0.4271679013 284 0.015 -1.338 -1.242 0.846 0.115 -0.175 0.4269384756 285 0.015 -1.346 -1.242 0.846 0.115 -0.175 0.4269299287 287 0.015 -1.345 -1.242 0.846 0.115 -0.175 0.4269297886 298 0.015 -1.345 -1.233 0.846 0.115 -0.175 0.4269192986 299 0.015 -1.345 -1.234 0.846 0.115 -0.175 0.4269183924 300 0.015 -1.345 -1.236 0.846 0.115 -0.175 0.4269180712 310 0.015 -1.345 -1.236 0.836 0.115 -0.175 0.4268888875 311 0.015 -1.345 -1.236 0.830 0.115 -0.175 0.4268828507 312 0.015 -1.345 -1.236 0.831 0.115 -0.175 0.4268825411 322 0.015 -1.345 -1.236 0.831 0.113 -0.175 0.4268682045 324 0.015 -1.345 -1.236 0.831 0.084 -0.175 0.4267981455 325 0.015 -1.345 -1.236 0.831 0.092 -0.175 0.4267814279 335 0.015 -1.345 -1.236 0.831 0.092 -0.220 0.4266079576 337 0.015 -1.345 -1.236 0.831 0.092 -0.222 0.4266074558 powell nthiter 4: fret = 0.426607 351 0.016 -1.345 -1.236 0.831 0.092 -0.223 0.4266060795 352 0.018 -1.345 -1.236 0.831 0.092 -0.223 0.4266055912 362 0.018 -1.360 -1.236 0.831 0.092 -0.223 0.4265525660 363 0.018 -1.362 -1.236 0.831 0.092 -0.223 0.4265517764 373 0.018 -1.362 -1.232 0.831 0.092 -0.223 0.4265436425 374 0.018 -1.362 -1.230 0.831 0.092 -0.223 0.4265424938 384 0.018 -1.362 -1.230 0.822 0.092 -0.223 0.4265327643 385 0.018 -1.362 -1.230 0.823 0.092 -0.223 0.4265327008 398 0.018 -1.362 -1.230 0.823 0.090 -0.223 0.4265325320 407 0.018 -1.362 -1.230 0.823 0.090 -0.227 0.4265295628 408 0.018 -1.362 -1.230 0.823 0.090 -0.228 0.4265293326 409 0.018 -1.362 -1.230 0.823 0.090 -0.229 0.4265291949 powell nthiter 5: fret = 0.426529 423 0.019 -1.362 -1.230 0.823 0.090 -0.229 0.4265285215 434 0.019 -1.363 -1.230 0.823 0.090 -0.229 0.4265278461 445 0.019 -1.363 -1.229 0.823 0.090 -0.229 0.4265276962 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 1.034048 1 -25.0 -25.0 25.0 1.053806 2 -25.0 25.0 -25.0 1.022925 3 -25.0 25.0 25.0 0.997445 4 25.0 -25.0 -25.0 1.032157 5 25.0 -25.0 25.0 1.010976 6 25.0 25.0 -25.0 1.045170 7 25.0 25.0 25.0 1.000933 REL: 8 0.426528 8.197459 1.024682 rel = 0.416254 Number of iterations 5 Min cost was 0.426528 Number of FunctionCalls 483 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.405761 sec Parameters at optimum (transmm) 0.01929 -1.36273 -1.22873 Parameters at optimum (rotdeg) 0.82332 0.09098 -0.22933 Final costs ---------------- Number of surface hits 2399 WM Intensity 9533.2076 +/- 1211.1061 Ctx Intensity 10045.5121 +/- 1584.0863 Pct Contrast 4.3825 +/- 16.7420 Cost 0.4265 RelCost 0.5597 Reg at min cost was 0.99992 0.01073 -0.00672 -3.46350; 0.01024 -0.37380 0.92745 -24.19487; -0.00744 0.92745 0.37388 15.91868; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/005/tmp.bbregister.75830/bbr.pass1.dat, type = 14 Original Reg 0.99988 0.01075 -0.01103 -3.41860; 0.01416 -0.36039 0.93269 -22.59723; -0.00606 0.93274 0.36050 17.46851; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00004 0.00002 -0.00431 0.04490; 0.00392 0.01341 0.00524 1.59764; 0.00138 0.00529 -0.01338 1.54983; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 1.741767 Computing change in rh position Surface-RMS-Diff-mm 1.816883 0.494704 2.969280 mri_segreg done mri_segreg --mov bold/005/tmp.bbregister.75830/template.nii --init-reg bold/005/tmp.bbregister.75830/bbr.pass1.dat --out-reg bold/005/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/005/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/005/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/005/tmp.bbregister.75830/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 mri_segreg --mov bold/005/tmp.bbregister.75830/template.nii --init-reg bold/005/tmp.bbregister.75830/bbr.pass1.dat --out-reg bold/005/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/005/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/005/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/005/tmp.bbregister.75830/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/005/tmp.bbregister.75830/template.nii regfile bold/005/tmp.bbregister.75830/bbr.pass1.dat subject 20231006_da047 dof 6 outregfile bold/005/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750396372 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99992 0.01073 -0.00672 -3.46350; 0.01024 -0.37380 0.92745 -24.19487; -0.00744 0.92745 0.37388 15.91868; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.036111 1 -25.0 -25.0 25.0 1.046143 2 -25.0 25.0 -25.0 1.017928 3 -25.0 25.0 25.0 1.017286 4 25.0 -25.0 -25.0 1.024661 5 25.0 -25.0 25.0 1.003433 6 25.0 25.0 -25.0 1.015737 7 25.0 25.0 25.0 1.025548 REL: 8 0.422498 8.186847 1.023356 rel = 0.412855 Initial costs ---------------- Number of surface hits 239836 WM Intensity 9524.2404 +/- 1198.0378 Ctx Intensity 10062.5629 +/- 1532.0549 Pct Contrast 4.8256 +/- 16.2637 Cost 0.4225 RelCost 0.4129 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.4343 0.4343 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.4318 0.4318 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.4316 0.4316 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.4303 0.4303 0.0 15 -0.1000 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.4293 0.4293 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.4290 0.4290 0.0 88 -0.1000 0.0000 -0.1000 -0.1000 0.1000 0.0000 0.4289 0.4289 0.0 96 -0.1000 0.0000 -0.1000 0.0000 0.1000 -0.1000 0.4277 0.4277 0.0 97 -0.1000 0.0000 -0.1000 0.0000 0.1000 0.0000 0.4271 0.4271 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.4265 0.4265 0.0 Brute Force -------------------------- Min cost was 0.426528 Number of iterations 729 Search time 0.793031 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.422498 7 0.189 0.000 0.000 0.000 0.000 0.000 0.4193637777 9 0.185 0.000 0.000 0.000 0.000 0.000 0.4193626747 18 0.185 0.382 0.000 0.000 0.000 0.000 0.4154238591 19 0.185 0.263 0.000 0.000 0.000 0.000 0.4143952120 28 0.185 0.263 -0.078 0.000 0.000 0.000 0.4139838797 29 0.185 0.263 -0.080 0.000 0.000 0.000 0.4139831917 38 0.185 0.263 -0.080 0.048 0.000 0.000 0.4138231649 39 0.185 0.263 -0.080 0.055 0.000 0.000 0.4138152625 40 0.185 0.263 -0.080 0.068 0.000 0.000 0.4138125282 42 0.185 0.263 -0.080 0.063 0.000 0.000 0.4138106087 44 0.185 0.263 -0.080 0.064 0.000 0.000 0.4138104909 52 0.185 0.263 -0.080 0.064 0.149 0.000 0.4124001285 53 0.185 0.263 -0.080 0.064 0.152 0.000 0.4123986706 54 0.185 0.263 -0.080 0.064 0.156 0.000 0.4123983709 56 0.185 0.263 -0.080 0.064 0.154 0.000 0.4123980168 64 0.185 0.263 -0.080 0.064 0.154 0.122 0.4117085635 65 0.185 0.263 -0.080 0.064 0.154 0.128 0.4117067108 powell nthiter 1: fret = 0.411707 75 0.239 0.263 -0.080 0.064 0.154 0.129 0.4112753506 76 0.254 0.263 -0.080 0.064 0.154 0.129 0.4112510781 77 0.256 0.263 -0.080 0.064 0.154 0.129 0.4112508178 78 0.257 0.263 -0.080 0.064 0.154 0.129 0.4112507663 87 0.257 0.267 -0.080 0.064 0.154 0.129 0.4112501830 89 0.257 0.266 -0.080 0.064 0.154 0.129 0.4112500499 97 0.257 0.266 -0.111 0.064 0.154 0.129 0.4111689816 99 0.257 0.266 -0.112 0.064 0.154 0.129 0.4111688657 107 0.257 0.266 -0.112 0.047 0.154 0.129 0.4111550197 108 0.257 0.266 -0.112 0.048 0.154 0.129 0.4111549618 109 0.257 0.266 -0.112 0.049 0.154 0.129 0.4111547994 119 0.257 0.266 -0.112 0.049 0.150 0.129 0.4111529753 120 0.257 0.266 -0.112 0.049 0.148 0.129 0.4111528490 121 0.257 0.266 -0.112 0.049 0.147 0.129 0.4111528015 129 0.257 0.266 -0.112 0.049 0.147 0.147 0.4111322466 130 0.257 0.266 -0.112 0.049 0.147 0.152 0.4111308605 131 0.257 0.266 -0.112 0.049 0.147 0.153 0.4111307721 132 0.257 0.266 -0.112 0.049 0.147 0.154 0.4111307672 powell nthiter 2: fret = 0.411131 143 0.261 0.266 -0.112 0.049 0.147 0.154 0.4111279708 152 0.261 0.267 -0.112 0.049 0.147 0.154 0.4111273666 153 0.261 0.271 -0.112 0.049 0.147 0.154 0.4111267193 155 0.261 0.270 -0.112 0.049 0.147 0.154 0.4111266622 173 0.261 0.270 -0.112 0.050 0.147 0.154 0.4111264222 179 0.261 0.270 -0.112 0.051 0.147 0.154 0.4111263801 180 0.261 0.270 -0.112 0.052 0.147 0.154 0.4111263427 powell nthiter 3: fret = 0.411126 253 0.261 0.270 -0.112 0.052 0.147 0.154 0.4111262921 powell nthiter 4: fret = 0.411126 281 0.261 0.270 -0.113 0.052 0.147 0.154 0.4111262856 290 0.261 0.270 -0.113 0.051 0.147 0.154 0.4111262642 powell nthiter 5: fret = 0.411126 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 1.037035 1 -25.0 -25.0 25.0 1.045894 2 -25.0 25.0 -25.0 1.018815 3 -25.0 25.0 25.0 1.017417 4 25.0 -25.0 -25.0 1.023804 5 25.0 -25.0 25.0 1.004213 6 25.0 25.0 -25.0 1.018167 7 25.0 25.0 25.0 1.025664 REL: 8 0.411126 8.191008 1.023876 rel = 0.401539 Number of iterations 5 Min cost was 0.411126 Number of FunctionCalls 365 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 16.057429 sec Parameters at optimum (transmm) 0.26137 0.26954 -0.11336 Parameters at optimum (rotdeg) 0.05112 0.14749 0.15440 Final costs ---------------- Number of surface hits 239836 WM Intensity 9529.9153 +/- 1182.0665 Ctx Intensity 10086.9143 +/- 1512.9489 Pct Contrast 5.0277 +/- 16.1501 Cost 0.4111 RelCost 0.4129 Reg at min cost was 0.99987 0.01413 -0.00825 -3.09595; 0.01295 -0.37459 0.92710 -23.94866; -0.01001 0.92708 0.37473 15.79259; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/005/register.dof6.dat, type = 14 Original Reg 0.99992 0.01073 -0.00672 -3.46350; 0.01024 -0.37380 0.92745 -24.19487; -0.00744 0.92745 0.37388 15.91868; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00005 -0.00340 0.00153 -0.36755; -0.00270 0.00079 0.00035 -0.24621; 0.00256 0.00036 -0.00084 0.12609; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.341569 Computing change in rh position Surface-RMS-Diff-mm 0.404059 0.101551 0.624911 mri_segreg done MinCost: 0.411126 9529.915276 10086.914273 5.027685 tkregister2_cmdl --mov bold/005/template.nii.gz --reg bold/005/register.dof6.dat --noedit --ltaout bold/005/register.dof6.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/005/template.nii.gz reg file bold/005/register.dof6.dat LoadVol 0 ZeroCRAS 0 7.4.1 Diagnostic Level -1 ---- Input registration matrix -------- 0.99987 0.01413 -0.00825 -3.09595; 0.01295 -0.37459 0.92710 -23.94866; -0.01001 0.92708 0.37473 15.79259; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: This is an unsigined short. INFO: loading target /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/005/template.nii.gz INFO: This is an unsigined short. Tmov: -------------------- -2.00000 0.00000 0.00000 110.00000; 0.00000 0.00000 2.00000 -60.00000; 0.00000 -2.00000 0.00000 110.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99987 0.01413 -0.00825 -3.09595; 0.01295 -0.37459 0.92710 -23.94866; -0.01001 0.92708 0.37473 15.79259; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = 20231006_da047 RegMat --------------------------- 0.99987 0.01413 -0.00825 -3.09595; 0.01295 -0.37459 0.92710 -23.94866; -0.01001 0.92708 0.37473 15.79259; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Wed Jun 18 10:10:19 EDT 2025 Ended at Wed Jun 18 10:11:15 EDT 2025 BBR-Run-Time-Sec 55 bbregister Done To check results, run: tkregisterfv --mov bold/005/template.nii.gz --reg bold/005/register.dof6.lta --surfs --sd /Volumes/umms-hillmera/asem_ptsd/DA047 Run: 006 ---------------- Wed Jun 18 10:11:15 EDT 2025 -------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 bbregister --s 20231006_da047 --init-coreg --6 --bold --mov bold/006/template.nii.gz --reg bold/006/register.dof6.dat --lta bold/006/register.dof6.lta --init-reg-out bold/006/init.register.dof6.dat tmp bold/006/tmp.bbregister.75931 Log file is bold/006/register.dof6.log Wed Jun 18 10:11:15 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 /Applications/freesurfer/bin/bbregister --s 20231006_da047 --init-coreg --6 --bold --mov bold/006/template.nii.gz --reg bold/006/register.dof6.dat --lta bold/006/register.dof6.lta --init-reg-out bold/006/init.register.dof6.dat FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 FREESURFER_HOME /Applications/freesurfer mri_convert bold/006/template.nii.gz bold/006/tmp.bbregister.75931/template.nii mri_convert bold/006/template.nii.gz bold/006/tmp.bbregister.75931/template.nii reading from bold/006/template.nii.gz... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) writing to bold/006/tmp.bbregister.75931/template.nii... mri_coreg --s 20231006_da047 --mov bold/006/tmp.bbregister.75931/template.nii --regdat bold/006/tmp.bbregister.75931/reg.init.dat --reg bold/006/tmp.bbregister.75931/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 cmdline mri_coreg --s 20231006_da047 --mov bold/006/tmp.bbregister.75931/template.nii --regdat bold/006/tmp.bbregister.75931/reg.init.dat --reg bold/006/tmp.bbregister.75931/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov bold/006/tmp.bbregister.75931/template.nii INFO: This is an unsigined short. Reading in ref /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/brainmask.mgz Reading in and applying refmask /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz Setting cras translation parameters to align volume centers Init matrix params 0.5000 4.0430 1.1597 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 -0.50000; 0.00000 1.00000 0.00000 -4.04302; 0.00000 0.00000 1.00000 -1.15972; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt 0.5000 4.0430 1.1597 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 18174.0000 mov gstd 1.6917 1.6917 1.6917 Smoothing mov refsat = 115.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0298185226 nhits = 87541 out of 16777216, Percent Overlap: 33.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 0.50000; 0.00000 1.00000 0.00000 4.04302; 0.00000 0.00000 1.00000 1.15972; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.50000 0.00000 0.00000 -9.25000; 0.00000 0.20017 -0.45818 87.39588; 0.00000 -0.45818 -0.20017 113.44038; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -3.50000 32.04302 -12.84028 2.00000 0.00000 0.00000 -1.0438722 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: -3.500000 32.043022 -12.840283 2.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0695934296 #@# 4 188 -3.50000 32.04302 -12.84028 2.00000 0.00000 0.00000 -1.0695934 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.069593 #@# 4 195 -3.46305 32.04302 -12.84028 2.00000 0.00000 0.00000 -1.0695945 #@# 4 196 -3.44048 32.04302 -12.84028 2.00000 0.00000 0.00000 -1.0695956 #@# 4 198 -3.38439 32.04302 -12.84028 2.00000 0.00000 0.00000 -1.0695965 #@# 4 199 -3.39439 32.04302 -12.84028 2.00000 0.00000 0.00000 -1.0695968 #@# 4 203 -3.39439 30.42499 -12.84028 2.00000 0.00000 0.00000 -1.0722625 #@# 4 206 -3.39439 28.00756 -12.84028 2.00000 0.00000 0.00000 -1.0739411 #@# 4 208 -3.39439 28.27655 -12.84028 2.00000 0.00000 0.00000 -1.0739771 #@# 4 209 -3.39439 28.33331 -12.84028 2.00000 0.00000 0.00000 -1.0739803 #@# 4 211 -3.39439 28.35264 -12.84028 2.00000 0.00000 0.00000 -1.0739827 #@# 4 215 -3.39439 28.35264 -14.45832 2.00000 0.00000 0.00000 -1.0751308 #@# 4 216 -3.39439 28.35264 -14.57229 2.00000 0.00000 0.00000 -1.0751345 #@# 4 221 -3.39439 28.35264 -14.52876 2.00000 0.00000 0.00000 -1.0751346 #@# 4 223 -3.39439 28.35264 -14.50185 2.00000 0.00000 0.00000 -1.0751352 #@# 4 224 -3.39439 28.35264 -14.48522 2.00000 0.00000 0.00000 -1.0751396 #@# 4 228 -3.39439 28.35264 -14.48522 0.38197 0.00000 0.00000 -1.0762107 #@# 4 229 -3.39439 28.35264 -14.48522 -1.15616 0.00000 0.00000 -1.0762258 #@# 4 230 -3.39439 28.35264 -14.48522 -0.41073 0.00000 0.00000 -1.0763446 #@# 4 234 -3.39439 28.35264 -14.48522 -0.39855 0.00000 0.00000 -1.0763457 #@# 4 237 -3.39439 28.35264 -14.48522 -0.38855 0.00000 0.00000 -1.0763462 #@# 4 241 -3.39439 28.35264 -14.48522 -0.38855 -1.61803 0.00000 -1.0763575 #@# 4 242 -3.39439 28.35264 -14.48522 -0.38855 -0.83343 0.00000 -1.0764406 #@# 4 254 -3.39439 28.35264 -14.48522 -0.38855 -0.83343 0.38197 -1.0764734 #@# 4 255 -3.39439 28.35264 -14.48522 -0.38855 -0.83343 0.27885 -1.0764757 #@# 4 256 -3.39439 28.35264 -14.48522 -0.38855 -0.83343 0.30082 -1.0764765 powell nthiter 1: fret = -1.076476 #@# 4 266 -3.31563 28.35264 -14.48522 -0.38855 -0.83343 0.30082 -1.0764782 #@# 4 267 -3.33665 28.35264 -14.48522 -0.38855 -0.83343 0.30082 -1.0764786 #@# 4 268 -3.34665 28.35264 -14.48522 -0.38855 -0.83343 0.30082 -1.0764787 #@# 4 274 -3.34665 27.73461 -14.48522 -0.38855 -0.83343 0.30082 -1.0766742 #@# 4 276 -3.34665 27.71466 -14.48522 -0.38855 -0.83343 0.30082 -1.0766770 #@# 4 281 -3.34665 27.71466 -13.48522 -0.38855 -0.83343 0.30082 -1.0769522 #@# 4 285 -3.34665 27.71466 -13.86719 -0.38855 -0.83343 0.30082 -1.0770011 #@# 4 286 -3.34665 27.71466 -13.78082 -0.38855 -0.83343 0.30082 -1.0770068 #@# 4 287 -3.34665 27.71466 -13.77082 -0.38855 -0.83343 0.30082 -1.0770073 #@# 4 289 -3.34665 27.71466 -13.72915 -0.38855 -0.83343 0.30082 -1.0770098 #@# 4 297 -3.34665 27.71466 -13.72915 -1.00659 -0.83343 0.30082 -1.0771625 #@# 4 299 -3.34665 27.71466 -13.72915 -1.17467 -0.83343 0.30082 -1.0771700 #@# 4 300 -3.34665 27.71466 -13.72915 -1.18467 -0.83343 0.30082 -1.0771707 #@# 4 320 -3.34665 27.71466 -13.72915 -1.18467 -0.82343 0.39967 -1.0771779 #@# 4 322 -3.34665 27.71466 -13.72915 -1.18467 -0.82343 0.38967 -1.0771782 powell nthiter 2: fret = -1.077178 #@# 4 332 -3.27852 27.71466 -13.72915 -1.18467 -0.82343 0.38967 -1.0771863 #@# 4 352 -3.27852 27.71466 -13.59445 -1.18467 -0.82343 0.38967 -1.0771960 #@# 4 353 -3.27852 27.71466 -13.60445 -1.18467 -0.82343 0.38967 -1.0771983 #@# 4 362 -3.27852 27.71466 -13.60445 -1.24704 -0.82343 0.38967 -1.0772021 #@# 4 364 -3.27852 27.71466 -13.60445 -1.29897 -0.82343 0.38967 -1.0772043 #@# 4 367 -3.27852 27.71466 -13.60445 -1.27914 -0.82343 0.38967 -1.0772085 #@# 4 378 -3.27852 27.71466 -13.60445 -1.27914 -0.83343 0.38967 -1.0772089 #@# 4 380 -3.27852 27.71466 -13.60445 -1.27914 -0.84343 0.38967 -1.0772102 Powell done niters total = 2 OptTimeSec 7.8 sec OptTimeMin 0.13 min nEvals 391 Final optimized parameters -3.27852368 27.71466446 -13.60445499 -1.27913558 -0.84342921 0.38966766 Final matrix parameters -3.2785 27.7147 -13.6045 -1.2791 -0.8434 0.3797 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.077210190988069 --------------------------------- Final RefRAS-to-MovRAS 0.99987 0.00680 -0.01472 -3.27852; -0.00713 0.99973 -0.02232 27.71466; 0.01456 0.02242 0.99964 -13.60445; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.49993 -0.00736 -0.00340 -5.97502; -0.00035 0.18988 -0.46254 81.42689; -0.00810 -0.46249 -0.18985 102.20290; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters -3.2785 27.7147 -13.6045 -1.2791 -0.8434 0.3897 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters -3.2785 27.7147 -13.6045 -1.2791 -0.8434 0.3897 nhits = 85872 out of 16777216, Percent Overlap: 32.8 mri_coreg RunTimeSec 32.4 sec To check run: tkregisterfv --mov bold/006/tmp.bbregister.75931/template.nii --targ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/brainmask.mgz --reg bold/006/tmp.bbregister.75931/mri_coreg.lta --s 20231006_da047 --surfs mri_coreg done mri_segreg --mov bold/006/tmp.bbregister.75931/template.nii --init-reg bold/006/tmp.bbregister.75931/reg.init.dat --out-reg bold/006/tmp.bbregister.75931/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 mri_segreg --mov bold/006/tmp.bbregister.75931/template.nii --init-reg bold/006/tmp.bbregister.75931/reg.init.dat --out-reg bold/006/tmp.bbregister.75931/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/006/tmp.bbregister.75931/template.nii regfile bold/006/tmp.bbregister.75931/reg.init.dat subject 20231006_da047 dof 6 outregfile bold/006/tmp.bbregister.75931/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750582002 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99987 0.00680 -0.01472 -3.27852; 0.01620 -0.37969 0.92497 -24.66461; -0.00070 0.92509 0.37975 17.03899; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.056994 1 -25.0 -25.0 25.0 1.056453 2 -25.0 25.0 -25.0 1.006891 3 -25.0 25.0 25.0 0.988997 4 25.0 -25.0 -25.0 1.015245 5 25.0 -25.0 25.0 1.027259 6 25.0 25.0 -25.0 1.026390 7 25.0 25.0 25.0 1.033129 REL: 8 0.567871 8.211358 1.026420 rel = 0.553254 Initial costs ---------------- Number of surface hits 2399 WM Intensity 9485.1692 +/- 1114.4800 Ctx Intensity 9874.9491 +/- 1437.5091 Pct Contrast 3.4744 +/- 14.7248 Cost 0.5679 RelCost 0.5533 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0392 1.0392 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 1.0368 1.0368 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.9964 0.9964 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9608 0.9608 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9295 0.9295 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.9050 0.9050 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8649 0.8649 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.8275 0.8275 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8116 0.8116 0.0 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.7570 0.7570 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5679 0.5679 0.0 Brute Force -------------------------- Min cost was 0.567871 Number of iterations 729 Search time 0.611239 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.567871 7 0.117 0.000 0.000 0.000 0.000 0.000 0.5661610718 8 0.126 0.000 0.000 0.000 0.000 0.000 0.5661474619 10 0.125 0.000 0.000 0.000 0.000 0.000 0.5661472917 14 0.125 -1.618 0.000 0.000 0.000 0.000 0.5543510320 15 0.125 -0.892 0.000 0.000 0.000 0.000 0.5388408987 19 0.125 -0.975 0.000 0.000 0.000 0.000 0.5384874413 21 0.125 -0.954 0.000 0.000 0.000 0.000 0.5384364392 23 0.125 -0.962 0.000 0.000 0.000 0.000 0.5384046827 24 0.125 -0.961 0.000 0.000 0.000 0.000 0.5384037604 28 0.125 -0.961 -1.618 0.000 0.000 0.000 0.5026447197 29 0.125 -0.961 -1.080 0.000 0.000 0.000 0.4905504628 33 0.125 -0.961 -1.074 0.000 0.000 0.000 0.4904973125 34 0.125 -0.961 -0.919 0.000 0.000 0.000 0.4887085151 39 0.125 -0.961 -0.918 0.000 0.000 0.000 0.4887082673 41 0.125 -0.961 -0.918 1.000 0.000 0.000 0.4509507344 46 0.125 -0.961 -0.918 0.987 0.000 0.000 0.4507175918 47 0.125 -0.961 -0.918 0.891 0.000 0.000 0.4503293536 49 0.125 -0.961 -0.918 0.924 0.000 0.000 0.4501340835 58 0.125 -0.961 -0.918 0.924 0.382 0.000 0.4450738854 59 0.125 -0.961 -0.918 0.924 0.350 0.000 0.4450323051 61 0.125 -0.961 -0.918 0.924 0.217 0.000 0.4449806106 66 0.125 -0.961 -0.918 0.924 0.224 0.000 0.4449739110 73 0.125 -0.961 -0.918 0.924 0.224 -0.618 0.4268596698 76 0.125 -0.961 -0.918 0.924 0.224 -0.684 0.4266233026 78 0.125 -0.961 -0.918 0.924 0.224 -0.668 0.4265964293 82 0.125 -0.961 -0.918 0.924 0.224 -0.664 0.4265943577 84 0.125 -0.961 -0.918 0.924 0.224 -0.665 0.4265942107 powell nthiter 1: fret = 0.426594 94 0.112 -0.961 -0.918 0.924 0.224 -0.665 0.4265685156 95 0.113 -0.961 -0.918 0.924 0.224 -0.665 0.4265675894 96 0.115 -0.961 -0.918 0.924 0.224 -0.665 0.4265673574 105 0.115 -1.067 -0.918 0.924 0.224 -0.665 0.4250152168 109 0.115 -1.068 -0.918 0.924 0.224 -0.665 0.4250150708 121 0.115 -1.068 -0.945 0.924 0.224 -0.665 0.4249592161 122 0.115 -1.068 -0.940 0.924 0.224 -0.665 0.4249443756 123 0.115 -1.068 -0.936 0.924 0.224 -0.665 0.4249385634 125 0.115 -1.068 -0.934 0.924 0.224 -0.665 0.4249369808 134 0.115 -1.068 -0.934 0.885 0.224 -0.665 0.4246547578 136 0.115 -1.068 -0.934 0.878 0.224 -0.665 0.4246513954 137 0.115 -1.068 -0.934 0.880 0.224 -0.665 0.4246510074 145 0.115 -1.068 -0.934 0.880 0.241 -0.665 0.4245238226 146 0.115 -1.068 -0.934 0.880 0.267 -0.665 0.4244088372 148 0.115 -1.068 -0.934 0.880 0.292 -0.665 0.4243506024 149 0.115 -1.068 -0.934 0.880 0.307 -0.665 0.4243286491 153 0.115 -1.068 -0.934 0.880 0.308 -0.665 0.4243284673 155 0.115 -1.068 -0.934 0.880 0.312 -0.665 0.4243278127 166 0.115 -1.068 -0.934 0.880 0.312 -0.667 0.4243273113 167 0.115 -1.068 -0.934 0.880 0.312 -0.666 0.4243268743 powell nthiter 2: fret = 0.424327 177 0.100 -1.068 -0.934 0.880 0.312 -0.666 0.4242879342 179 0.104 -1.068 -0.934 0.880 0.312 -0.666 0.4242823396 180 0.103 -1.068 -0.934 0.880 0.312 -0.666 0.4242822958 189 0.103 -1.067 -0.934 0.880 0.312 -0.666 0.4242820725 198 0.103 -1.067 -0.958 0.880 0.312 -0.666 0.4241541312 200 0.103 -1.067 -0.967 0.880 0.312 -0.666 0.4241389585 202 0.103 -1.067 -0.966 0.880 0.312 -0.666 0.4241380998 204 0.103 -1.067 -0.965 0.880 0.312 -0.666 0.4241380047 214 0.103 -1.067 -0.965 0.883 0.312 -0.666 0.4241379674 225 0.103 -1.067 -0.965 0.883 0.317 -0.666 0.4241363173 226 0.103 -1.067 -0.965 0.883 0.316 -0.666 0.4241360934 236 0.103 -1.067 -0.965 0.883 0.316 -0.678 0.4241305251 237 0.103 -1.067 -0.965 0.883 0.316 -0.673 0.4241293081 238 0.103 -1.067 -0.965 0.883 0.316 -0.674 0.4241290504 powell nthiter 3: fret = 0.424129 251 0.102 -1.067 -0.965 0.883 0.316 -0.674 0.4241289587 259 0.102 -1.045 -0.965 0.883 0.316 -0.674 0.4240805788 260 0.102 -1.047 -0.965 0.883 0.316 -0.674 0.4240786778 261 0.102 -1.049 -0.965 0.883 0.316 -0.674 0.4240770571 263 0.102 -1.052 -0.965 0.883 0.316 -0.674 0.4240763458 264 0.102 -1.051 -0.965 0.883 0.316 -0.674 0.4240762984 272 0.102 -1.051 -0.981 0.883 0.316 -0.674 0.4240561069 274 0.102 -1.051 -0.977 0.883 0.316 -0.674 0.4240558563 275 0.102 -1.051 -0.979 0.883 0.316 -0.674 0.4240549714 296 0.102 -1.051 -0.979 0.883 0.337 -0.674 0.4240097270 312 0.102 -1.051 -0.979 0.883 0.337 -0.672 0.4240097197 317 0.101 -1.036 -0.993 0.883 0.358 -0.670 0.4239829889 323 0.102 -1.042 -0.988 0.883 0.350 -0.671 0.4239769793 325 0.102 -1.040 -0.989 0.883 0.352 -0.671 0.4239747629 327 0.102 -1.040 -0.989 0.883 0.352 -0.671 0.4239746356 328 0.102 -1.040 -0.989 0.883 0.352 -0.671 0.4239741778 330 0.102 -1.040 -0.989 0.883 0.352 -0.671 0.4239740567 powell nthiter 4: fret = 0.423974 342 0.100 -1.040 -0.989 0.883 0.352 -0.671 0.4239736027 362 0.100 -1.040 -0.990 0.883 0.352 -0.671 0.4239692477 363 0.100 -1.040 -1.005 0.883 0.352 -0.671 0.4239383565 374 0.100 -1.040 -1.005 0.870 0.352 -0.671 0.4239209280 375 0.100 -1.040 -1.005 0.869 0.352 -0.671 0.4239202350 391 0.099 -1.024 -1.019 0.869 0.373 -0.669 0.4239162513 395 0.100 -1.030 -1.013 0.869 0.365 -0.670 0.4239016161 396 0.100 -1.031 -1.013 0.869 0.364 -0.670 0.4239010048 397 0.100 -1.032 -1.012 0.869 0.363 -0.670 0.4239003698 404 0.100 -1.032 -1.012 0.869 0.363 -0.670 0.4239003439 powell nthiter 5: fret = 0.423900 415 0.098 -1.032 -1.012 0.869 0.363 -0.670 0.4238983518 416 0.097 -1.032 -1.012 0.869 0.363 -0.670 0.4238976628 418 0.096 -1.032 -1.012 0.869 0.363 -0.670 0.4238975181 428 0.096 -1.032 -1.012 0.869 0.363 -0.667 0.4238973716 429 0.096 -1.032 -1.012 0.869 0.363 -0.666 0.4238968206 432 0.096 -1.032 -1.012 0.869 0.363 -0.663 0.4238958255 447 0.096 -1.032 -1.017 0.869 0.363 -0.663 0.4238957401 448 0.096 -1.032 -1.015 0.869 0.363 -0.663 0.4238944337 450 0.096 -1.032 -1.016 0.869 0.363 -0.663 0.4238943644 459 0.096 -1.032 -1.016 0.870 0.363 -0.663 0.4238943197 460 0.096 -1.032 -1.016 0.871 0.363 -0.663 0.4238940021 470 0.096 -1.032 -1.016 0.871 0.358 -0.663 0.4238858907 471 0.096 -1.032 -1.016 0.871 0.355 -0.663 0.4238840049 473 0.096 -1.032 -1.016 0.871 0.356 -0.663 0.4238838259 480 0.096 -1.026 -1.021 0.871 0.364 -0.662 0.4238708556 481 0.095 -1.025 -1.022 0.871 0.365 -0.662 0.4238678324 483 0.095 -1.023 -1.024 0.871 0.367 -0.662 0.4238652466 488 0.095 -1.023 -1.024 0.871 0.367 -0.662 0.4238650570 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 1.028585 1 -25.0 -25.0 25.0 1.067517 2 -25.0 25.0 -25.0 1.026669 3 -25.0 25.0 25.0 0.977555 4 25.0 -25.0 -25.0 1.042007 5 25.0 -25.0 25.0 1.007399 6 25.0 25.0 -25.0 1.025699 7 25.0 25.0 25.0 1.027894 REL: 8 0.423865 8.203325 1.025416 rel = 0.413359 Number of iterations 5 Min cost was 0.423865 Number of FunctionCalls 489 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.413817 sec Parameters at optimum (transmm) 0.09540 -1.02324 -1.02353 Parameters at optimum (rotdeg) 0.87107 0.36725 -0.66181 Final costs ---------------- Number of surface hits 2399 WM Intensity 9338.7950 +/- 1195.9743 Ctx Intensity 9845.4636 +/- 1535.1363 Pct Contrast 4.5780 +/- 16.3793 Cost 0.4239 RelCost 0.5533 Reg at min cost was 0.99997 0.00814 -0.00158 -3.36388; 0.00466 -0.39383 0.91917 -25.90574; -0.00686 0.91915 0.39386 15.65920; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/006/tmp.bbregister.75931/bbr.pass1.dat, type = 14 Original Reg 0.99987 0.00680 -0.01472 -3.27852; 0.01620 -0.37969 0.92497 -24.66461; -0.00070 0.92509 0.37975 17.03899; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00010 -0.00134 -0.01314 0.08537; 0.01154 0.01414 0.00580 1.24113; 0.00616 0.00594 -0.01410 1.37979; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 1.262575 Computing change in rh position Surface-RMS-Diff-mm 1.524242 0.581309 2.891261 mri_segreg done mri_segreg --mov bold/006/tmp.bbregister.75931/template.nii --init-reg bold/006/tmp.bbregister.75931/bbr.pass1.dat --out-reg bold/006/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/006/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/006/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/006/tmp.bbregister.75931/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 mri_segreg --mov bold/006/tmp.bbregister.75931/template.nii --init-reg bold/006/tmp.bbregister.75931/bbr.pass1.dat --out-reg bold/006/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/006/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/006/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/006/tmp.bbregister.75931/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/006/tmp.bbregister.75931/template.nii regfile bold/006/tmp.bbregister.75931/bbr.pass1.dat subject 20231006_da047 dof 6 outregfile bold/006/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750418761 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99997 0.00814 -0.00158 -3.36388; 0.00466 -0.39383 0.91917 -25.90574; -0.00686 0.91915 0.39386 15.65920; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.035651 1 -25.0 -25.0 25.0 1.053691 2 -25.0 25.0 -25.0 1.028198 3 -25.0 25.0 25.0 1.019171 4 25.0 -25.0 -25.0 1.030660 5 25.0 -25.0 25.0 0.993957 6 25.0 25.0 -25.0 1.015136 7 25.0 25.0 25.0 1.021322 REL: 8 0.423732 8.197786 1.024723 rel = 0.413509 Initial costs ---------------- Number of surface hits 239836 WM Intensity 9323.8147 +/- 1161.3574 Ctx Intensity 9854.0602 +/- 1471.1381 Pct Contrast 4.9231 +/- 15.6249 Cost 0.4237 RelCost 0.4135 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.4277 0.4277 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.4267 0.4267 0.0 10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.4265 0.4265 0.0 20 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.1000 0.4260 0.4260 0.0 82 -0.1000 0.0000 -0.1000 -0.1000 -0.1000 0.0000 0.4249 0.4249 0.0 266 0.0000 -0.1000 -0.1000 0.1000 0.0000 0.1000 0.4241 0.4241 0.0 338 0.0000 0.0000 -0.1000 0.0000 0.0000 0.1000 0.4238 0.4238 0.0 347 0.0000 0.0000 -0.1000 0.1000 0.0000 0.1000 0.4236 0.4236 0.0 590 0.1000 0.0000 -0.1000 0.1000 0.0000 0.1000 0.4235 0.4235 0.0 Brute Force -------------------------- Min cost was 0.423475 Number of iterations 729 Search time 0.794739 sec Parameters at best (transmm, rotdeg) 0.100 0.000 -0.100 0.100 0.000 0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0.1 1 0 2 -0.1 3 0.1 4 0 5 0.1 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.419628 8 0.105 0.000 -0.100 0.100 0.000 0.100 0.4196268748 9 0.104 0.000 -0.100 0.100 0.000 0.100 0.4196268503 17 0.104 -0.029 -0.100 0.100 0.000 0.100 0.4195066080 18 0.104 -0.047 -0.100 0.100 0.000 0.100 0.4194991543 19 0.104 -0.041 -0.100 0.100 0.000 0.100 0.4194956292 28 0.104 -0.041 -0.194 0.100 0.000 0.100 0.4189508978 29 0.104 -0.041 -0.192 0.100 0.000 0.100 0.4189497046 30 0.104 -0.041 -0.189 0.100 0.000 0.100 0.4189494417 33 0.104 -0.041 -0.190 0.100 0.000 0.100 0.4189492842 41 0.104 -0.041 -0.190 0.153 0.000 0.100 0.4187054694 42 0.104 -0.041 -0.190 0.168 0.000 0.100 0.4186907164 43 0.104 -0.041 -0.190 0.169 0.000 0.100 0.4186906829 44 0.104 -0.041 -0.190 0.170 0.000 0.100 0.4186906071 57 0.104 -0.041 -0.190 0.170 -0.056 0.100 0.4185642053 58 0.104 -0.041 -0.190 0.170 -0.045 0.100 0.4185596699 59 0.104 -0.041 -0.190 0.170 -0.047 0.100 0.4185593010 60 0.104 -0.041 -0.190 0.170 -0.048 0.100 0.4185592866 68 0.104 -0.041 -0.190 0.170 -0.048 0.218 0.4181190564 69 0.104 -0.041 -0.190 0.170 -0.048 0.211 0.4181147415 70 0.104 -0.041 -0.190 0.170 -0.048 0.206 0.4181131609 71 0.104 -0.041 -0.190 0.170 -0.048 0.205 0.4181130833 72 0.104 -0.041 -0.190 0.170 -0.048 0.204 0.4181130775 powell nthiter 1: fret = 0.418113 82 0.122 -0.041 -0.190 0.170 -0.048 0.204 0.4180845876 83 0.121 -0.041 -0.190 0.170 -0.048 0.204 0.4180845600 92 0.121 -0.043 -0.190 0.170 -0.048 0.204 0.4180842779 100 0.121 -0.043 -0.209 0.170 -0.048 0.204 0.4180644899 101 0.121 -0.043 -0.208 0.170 -0.048 0.204 0.4180641748 102 0.121 -0.043 -0.207 0.170 -0.048 0.204 0.4180639987 105 0.121 -0.043 -0.206 0.170 -0.048 0.204 0.4180639574 113 0.121 -0.043 -0.206 0.177 -0.048 0.204 0.4180625893 114 0.121 -0.043 -0.206 0.175 -0.048 0.204 0.4180624610 123 0.121 -0.043 -0.206 0.175 -0.054 0.204 0.4180606356 124 0.121 -0.043 -0.206 0.175 -0.053 0.204 0.4180604812 133 0.121 -0.043 -0.206 0.175 -0.053 0.212 0.4180556804 134 0.121 -0.043 -0.206 0.175 -0.053 0.214 0.4180554160 135 0.121 -0.043 -0.206 0.175 -0.053 0.215 0.4180553398 powell nthiter 2: fret = 0.418055 147 0.125 -0.043 -0.206 0.175 -0.053 0.215 0.4180550762 148 0.123 -0.043 -0.206 0.175 -0.053 0.215 0.4180547333 157 0.123 -0.040 -0.206 0.175 -0.053 0.215 0.4180540741 166 0.123 -0.040 -0.211 0.175 -0.053 0.215 0.4180537375 167 0.123 -0.040 -0.209 0.175 -0.053 0.215 0.4180537235 176 0.123 -0.040 -0.209 0.179 -0.053 0.215 0.4180534806 191 0.123 -0.040 -0.209 0.179 -0.055 0.215 0.4180533644 202 0.123 -0.040 -0.209 0.179 -0.055 0.216 0.4180533119 powell nthiter 3: fret = 0.418053 229 0.123 -0.040 -0.212 0.179 -0.055 0.216 0.4180531833 231 0.123 -0.040 -0.211 0.179 -0.055 0.216 0.4180531633 271 0.123 -0.040 -0.211 0.179 -0.055 0.216 0.4180531627 276 0.123 -0.040 -0.211 0.179 -0.055 0.216 0.4180531622 powell nthiter 4: fret = 0.418053 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.036516 1 -25.0 -25.0 25.0 1.053894 2 -25.0 25.0 -25.0 1.025189 3 -25.0 25.0 25.0 1.017894 4 25.0 -25.0 -25.0 1.028685 5 25.0 -25.0 25.0 0.994022 6 25.0 25.0 -25.0 1.015133 7 25.0 25.0 25.0 1.022622 REL: 8 0.418053 8.193954 1.024244 rel = 0.408158 Number of iterations 4 Min cost was 0.418053 Number of FunctionCalls 346 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 15.303978 sec Parameters at optimum (transmm) 0.12296 -0.04006 -0.21065 Parameters at optimum (rotdeg) 0.17892 -0.05494 0.21603 Final costs ---------------- Number of surface hits 239836 WM Intensity 9313.7376 +/- 1176.3265 Ctx Intensity 9847.4011 +/- 1500.1164 Pct Contrast 4.9243 +/- 16.1512 Cost 0.4181 RelCost 0.4135 Reg at min cost was 0.99995 0.00876 -0.00542 -3.15798; 0.00845 -0.39667 0.91792 -26.00713; -0.00589 0.91792 0.39672 15.36435; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/006/register.dof6.dat, type = 14 Original Reg 0.99997 0.00814 -0.00158 -3.36388; 0.00466 -0.39383 0.91917 -25.90574; -0.00686 0.91915 0.39386 15.65920; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00002 -0.00062 0.00384 -0.20591; -0.00379 0.00284 0.00125 0.10139; -0.00097 0.00123 -0.00287 0.29485; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.326889 Computing change in rh position Surface-RMS-Diff-mm 0.303317 0.112370 0.558759 mri_segreg done MinCost: 0.418053 9313.737635 9847.401123 4.924308 tkregister2_cmdl --mov bold/006/template.nii.gz --reg bold/006/register.dof6.dat --noedit --ltaout bold/006/register.dof6.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/006/template.nii.gz reg file bold/006/register.dof6.dat LoadVol 0 ZeroCRAS 0 7.4.1 Diagnostic Level -1 ---- Input registration matrix -------- 0.99995 0.00876 -0.00542 -3.15798; 0.00845 -0.39667 0.91792 -26.00713; -0.00589 0.91792 0.39672 15.36435; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: This is an unsigined short. INFO: loading target /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/006/template.nii.gz INFO: This is an unsigined short. Tmov: -------------------- -2.00000 0.00000 0.00000 110.00000; 0.00000 0.00000 2.00000 -60.00000; 0.00000 -2.00000 0.00000 110.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99995 0.00876 -0.00542 -3.15798; 0.00845 -0.39667 0.91792 -26.00713; -0.00589 0.91792 0.39672 15.36435; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = 20231006_da047 RegMat --------------------------- 0.99995 0.00876 -0.00542 -3.15798; 0.00845 -0.39667 0.91792 -26.00713; -0.00589 0.91792 0.39672 15.36435; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Wed Jun 18 10:11:15 EDT 2025 Ended at Wed Jun 18 10:12:10 EDT 2025 BBR-Run-Time-Sec 55 bbregister Done To check results, run: tkregisterfv --mov bold/006/template.nii.gz --reg bold/006/register.dof6.lta --surfs --sd /Volumes/umms-hillmera/asem_ptsd/DA047 Run: 007 ---------------- Wed Jun 18 10:12:10 EDT 2025 -------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 bbregister --s 20231006_da047 --init-coreg --6 --bold --mov bold/007/template.nii.gz --reg bold/007/register.dof6.dat --lta bold/007/register.dof6.lta --init-reg-out bold/007/init.register.dof6.dat tmp bold/007/tmp.bbregister.76040 Log file is bold/007/register.dof6.log Wed Jun 18 10:12:10 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 /Applications/freesurfer/bin/bbregister --s 20231006_da047 --init-coreg --6 --bold --mov bold/007/template.nii.gz --reg bold/007/register.dof6.dat --lta bold/007/register.dof6.lta --init-reg-out bold/007/init.register.dof6.dat FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 FREESURFER_HOME /Applications/freesurfer mri_convert bold/007/template.nii.gz bold/007/tmp.bbregister.76040/template.nii mri_convert bold/007/template.nii.gz bold/007/tmp.bbregister.76040/template.nii reading from bold/007/template.nii.gz... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) writing to bold/007/tmp.bbregister.76040/template.nii... mri_coreg --s 20231006_da047 --mov bold/007/tmp.bbregister.76040/template.nii --regdat bold/007/tmp.bbregister.76040/reg.init.dat --reg bold/007/tmp.bbregister.76040/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 cmdline mri_coreg --s 20231006_da047 --mov bold/007/tmp.bbregister.76040/template.nii --regdat bold/007/tmp.bbregister.76040/reg.init.dat --reg bold/007/tmp.bbregister.76040/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov bold/007/tmp.bbregister.76040/template.nii INFO: This is an unsigined short. Reading in ref /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/brainmask.mgz Reading in and applying refmask /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz Setting cras translation parameters to align volume centers Init matrix params 0.5000 4.0430 1.1597 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 -0.50000; 0.00000 1.00000 0.00000 -4.04302; 0.00000 0.00000 1.00000 -1.15972; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt 0.5000 4.0430 1.1597 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 20089.0000 mov gstd 1.6917 1.6917 1.6917 Smoothing mov refsat = 115.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0299110303 nhits = 87541 out of 16777216, Percent Overlap: 33.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 0.50000; 0.00000 1.00000 0.00000 4.04302; 0.00000 0.00000 1.00000 1.15972; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.50000 0.00000 0.00000 -9.25000; 0.00000 0.20017 -0.45818 87.39588; 0.00000 -0.45818 -0.20017 113.44038; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -3.50000 32.04302 -12.84028 2.00000 0.00000 0.00000 -1.0442789 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: -3.500000 32.043022 -12.840283 2.000000 0.000000 0.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0698956251 #@# 4 188 -3.50000 32.04302 -12.84028 2.00000 0.00000 0.00000 -1.0698956 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.069896 #@# 4 195 -3.64255 32.04302 -12.84028 2.00000 0.00000 0.00000 -1.0699011 #@# 4 197 -3.61762 32.04302 -12.84028 2.00000 0.00000 0.00000 -1.0699015 #@# 4 203 -3.60046 30.42499 -12.84028 2.00000 0.00000 0.00000 -1.0726452 #@# 4 206 -3.60046 27.68977 -12.84028 2.00000 0.00000 0.00000 -1.0743701 #@# 4 208 -3.60046 28.17699 -12.84028 2.00000 0.00000 0.00000 -1.0745175 #@# 4 212 -3.60046 28.14626 -12.84028 2.00000 0.00000 0.00000 -1.0745212 #@# 4 219 -3.60046 28.14626 -14.45832 2.00000 0.00000 0.00000 -1.0758340 #@# 4 225 -3.60046 28.14626 -14.51933 2.00000 0.00000 0.00000 -1.0758381 #@# 4 226 -3.60046 28.14626 -14.59063 2.00000 0.00000 0.00000 -1.0758417 #@# 4 228 -3.60046 28.14626 -14.57534 2.00000 0.00000 0.00000 -1.0758481 #@# 4 232 -3.60046 28.14626 -14.57534 0.38197 0.00000 0.00000 -1.0769871 #@# 4 235 -3.60046 28.14626 -14.57534 -0.23967 0.00000 0.00000 -1.0771046 #@# 4 239 -3.60046 28.14626 -14.57534 -0.17562 0.00000 0.00000 -1.0771053 #@# 4 248 -3.60046 28.14626 -14.57534 -0.17562 -0.61803 0.00000 -1.0771807 #@# 4 252 -3.60046 28.14626 -14.57534 -0.17562 -0.60302 0.00000 -1.0771812 #@# 4 255 -3.60046 28.14626 -14.57534 -0.17562 -0.59302 0.00000 -1.0771813 powell nthiter 1: fret = -1.077181 #@# 4 275 -3.59046 28.14626 -14.57534 -0.17562 -0.59302 0.00000 -1.0771815 #@# 4 281 -3.59046 27.52822 -14.57534 -0.17562 -0.59302 0.00000 -1.0773352 #@# 4 283 -3.59046 27.58322 -14.57534 -0.17562 -0.59302 0.00000 -1.0773383 #@# 4 284 -3.59046 27.62243 -14.57534 -0.17562 -0.59302 0.00000 -1.0773401 #@# 4 292 -3.59046 27.62243 -13.57534 -0.17562 -0.59302 0.00000 -1.0775408 #@# 4 296 -3.59046 27.62243 -13.95730 -0.17562 -0.59302 0.00000 -1.0776324 #@# 4 298 -3.59046 27.62243 -13.91332 -0.17562 -0.59302 0.00000 -1.0776360 #@# 4 301 -3.59046 27.62243 -13.89470 -0.17562 -0.59302 0.00000 -1.0776367 #@# 4 305 -3.59046 27.62243 -13.89470 -1.79366 -0.59302 0.00000 -1.0776858 #@# 4 306 -3.59046 27.62243 -13.89470 -1.03806 -0.59302 0.00000 -1.0778381 #@# 4 310 -3.59046 27.62243 -13.89470 -1.01032 -0.59302 0.00000 -1.0778408 #@# 4 311 -3.59046 27.62243 -13.89470 -0.93693 -0.59302 0.00000 -1.0778419 #@# 4 313 -3.59046 27.62243 -13.89470 -0.96485 -0.59302 0.00000 -1.0778451 #@# 4 322 -3.59046 27.62243 -13.89470 -0.96485 -0.74407 0.00000 -1.0778459 #@# 4 323 -3.59046 27.62243 -13.89470 -0.96485 -0.68386 0.00000 -1.0778461 #@# 4 324 -3.59046 27.62243 -13.89470 -0.96485 -0.70198 0.00000 -1.0778470 #@# 4 335 -3.59046 27.62243 -13.89470 -0.96485 -0.70198 -0.01000 -1.0778475 powell nthiter 2: fret = -1.077847 #@# 4 346 -3.56772 27.62243 -13.89470 -0.96485 -0.70198 -0.01000 -1.0778489 #@# 4 347 -3.55772 27.62243 -13.89470 -0.96485 -0.70198 -0.01000 -1.0778493 #@# 4 355 -3.55772 27.59711 -13.89470 -0.96485 -0.70198 -0.01000 -1.0778509 #@# 4 365 -3.55772 27.59711 -13.73665 -0.96485 -0.70198 -0.01000 -1.0778650 #@# 4 367 -3.55772 27.59711 -13.65112 -0.96485 -0.70198 -0.01000 -1.0778691 #@# 4 369 -3.55772 27.59711 -13.66112 -0.96485 -0.70198 -0.01000 -1.0778720 Powell done niters total = 2 OptTimeSec 8.3 sec OptTimeMin 0.14 min nEvals 404 Final optimized parameters -3.55772281 27.59711075 -13.66112232 -0.96484566 -0.70198417 -0.01000000 Final matrix parameters -3.5577 27.5971 -13.6611 -0.9648 -0.7020 0.0027 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.077872025035334 --------------------------------- Final RefRAS-to-MovRAS 0.99992 -0.00017 -0.01225 -3.55772; -0.00003 0.99986 -0.01684 27.59711; 0.01225 0.01684 0.99978 -13.66112; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.49996 -0.00613 0.00009 -6.44340; 0.00244 0.19242 -0.46149 80.67463; -0.00562 -0.46145 -0.19243 102.08187; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters -3.5577 27.5971 -13.6611 -0.9648 -0.7020 -0.0100 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters -3.5577 27.5971 -13.6611 -0.9648 -0.7020 -0.0100 nhits = 85839 out of 16777216, Percent Overlap: 32.7 mri_coreg RunTimeSec 33.1 sec To check run: tkregisterfv --mov bold/007/tmp.bbregister.76040/template.nii --targ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/brainmask.mgz --reg bold/007/tmp.bbregister.76040/mri_coreg.lta --s 20231006_da047 --surfs mri_coreg done mri_segreg --mov bold/007/tmp.bbregister.76040/template.nii --init-reg bold/007/tmp.bbregister.76040/reg.init.dat --out-reg bold/007/tmp.bbregister.76040/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 mri_segreg --mov bold/007/tmp.bbregister.76040/template.nii --init-reg bold/007/tmp.bbregister.76040/reg.init.dat --out-reg bold/007/tmp.bbregister.76040/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/007/tmp.bbregister.76040/template.nii regfile bold/007/tmp.bbregister.76040/reg.init.dat subject 20231006_da047 dof 6 outregfile bold/007/tmp.bbregister.76040/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750448729 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99993 -0.00017 -0.01225 -3.55773; 0.01124 -0.38486 0.92291 -24.66948; 0.00488 0.92297 0.38483 16.90858; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.047289 1 -25.0 -25.0 25.0 1.029489 2 -25.0 25.0 -25.0 1.018896 3 -25.0 25.0 25.0 0.989118 4 25.0 -25.0 -25.0 1.037296 5 25.0 -25.0 25.0 1.010647 6 25.0 25.0 -25.0 1.032593 7 25.0 25.0 25.0 1.034290 REL: 8 0.604261 8.199618 1.024952 rel = 0.589551 Initial costs ---------------- Number of surface hits 2399 WM Intensity 9639.2285 +/- 1114.4104 Ctx Intensity 9989.8069 +/- 1459.7558 Pct Contrast 2.9209 +/- 15.3028 Cost 0.6043 RelCost 0.5896 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0654 1.0654 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0500 1.0500 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 1.0337 1.0337 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.9933 0.9933 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9531 0.9531 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9338 0.9338 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.9074 0.9074 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.9012 0.9012 0.0 105 -4.0000 0.0000 -4.0000 4.0000 4.0000 -4.0000 0.8887 0.8887 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8814 0.8814 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.8132 0.8132 0.0 337 0.0000 0.0000 -4.0000 0.0000 0.0000 0.0000 0.7926 0.7926 0.0 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.7660 0.7660 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.6043 0.6043 0.0 Brute Force -------------------------- Min cost was 0.604261 Number of iterations 729 Search time 0.611642 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.604261 7 0.107 0.000 0.000 0.000 0.000 0.000 0.6030777615 8 0.113 0.000 0.000 0.000 0.000 0.000 0.6030477570 9 0.158 0.000 0.000 0.000 0.000 0.000 0.6030307762 11 0.138 0.000 0.000 0.000 0.000 0.000 0.6030252285 12 0.143 0.000 0.000 0.000 0.000 0.000 0.6030178542 13 0.147 0.000 0.000 0.000 0.000 0.000 0.6030151656 14 0.149 0.000 0.000 0.000 0.000 0.000 0.6030134872 16 0.150 0.000 0.000 0.000 0.000 0.000 0.6030128348 20 0.150 -1.618 0.000 0.000 0.000 0.000 0.5620549047 21 0.150 -1.100 0.000 0.000 0.000 0.000 0.5509191922 25 0.150 -1.185 0.000 0.000 0.000 0.000 0.5503395437 26 0.150 -1.188 0.000 0.000 0.000 0.000 0.5503312698 27 0.150 -1.216 0.000 0.000 0.000 0.000 0.5502988710 29 0.150 -1.214 0.000 0.000 0.000 0.000 0.5502940245 30 0.150 -1.206 0.000 0.000 0.000 0.000 0.5502928894 32 0.150 -1.210 0.000 0.000 0.000 0.000 0.5502893330 33 0.150 -1.211 0.000 0.000 0.000 0.000 0.5502884360 37 0.150 -1.211 -1.618 0.000 0.000 0.000 0.4864379987 38 0.150 -1.211 -1.278 0.000 0.000 0.000 0.4777044611 42 0.150 -1.211 -1.187 0.000 0.000 0.000 0.4773924210 43 0.150 -1.211 -1.189 0.000 0.000 0.000 0.4773892425 44 0.150 -1.211 -1.202 0.000 0.000 0.000 0.4773463372 45 0.150 -1.211 -1.231 0.000 0.000 0.000 0.4772167207 47 0.150 -1.211 -1.227 0.000 0.000 0.000 0.4772145034 48 0.150 -1.211 -1.228 0.000 0.000 0.000 0.4772121418 51 0.150 -1.211 -1.228 1.000 0.000 0.000 0.4593972421 55 0.150 -1.211 -1.228 0.618 0.000 0.000 0.4571333446 56 0.150 -1.211 -1.228 0.755 0.000 0.000 0.4559173245 57 0.150 -1.211 -1.228 0.760 0.000 0.000 0.4558827330 59 0.150 -1.211 -1.228 0.803 0.000 0.000 0.4556918402 61 0.150 -1.211 -1.228 0.809 0.000 0.000 0.4556852218 62 0.150 -1.211 -1.228 0.810 0.000 0.000 0.4556848990 69 0.150 -1.211 -1.228 0.810 0.382 0.000 0.4531541693 70 0.150 -1.211 -1.228 0.810 0.261 0.000 0.4526747505 71 0.150 -1.211 -1.228 0.810 0.273 0.000 0.4525738540 72 0.150 -1.211 -1.228 0.810 0.304 0.000 0.4523978364 74 0.150 -1.211 -1.228 0.810 0.305 0.000 0.4523964215 75 0.150 -1.211 -1.228 0.810 0.308 0.000 0.4523923187 86 0.150 -1.211 -1.228 0.810 0.308 -0.285 0.4479620761 88 0.150 -1.211 -1.228 0.810 0.308 -0.298 0.4479537397 powell nthiter 1: fret = 0.447954 98 0.059 -1.211 -1.228 0.810 0.308 -0.298 0.4472543884 100 0.066 -1.211 -1.228 0.810 0.308 -0.298 0.4472493405 102 0.064 -1.211 -1.228 0.810 0.308 -0.298 0.4472491388 112 0.064 -1.181 -1.228 0.810 0.308 -0.298 0.4472229606 113 0.064 -1.191 -1.228 0.810 0.308 -0.298 0.4472051491 115 0.064 -1.190 -1.228 0.810 0.308 -0.298 0.4472036466 117 0.064 -1.189 -1.228 0.810 0.308 -0.298 0.4472028229 118 0.064 -1.188 -1.228 0.810 0.308 -0.298 0.4472026638 131 0.064 -1.188 -1.230 0.810 0.308 -0.298 0.4472016250 132 0.064 -1.188 -1.231 0.810 0.308 -0.298 0.4472015159 140 0.064 -1.188 -1.231 0.594 0.308 -0.298 0.4446557702 142 0.064 -1.188 -1.231 0.608 0.308 -0.298 0.4446379184 145 0.064 -1.188 -1.231 0.609 0.308 -0.298 0.4446373213 153 0.064 -1.188 -1.231 0.609 0.208 -0.298 0.4444925833 154 0.064 -1.188 -1.231 0.609 0.250 -0.298 0.4443822255 157 0.064 -1.188 -1.231 0.609 0.249 -0.298 0.4443820524 164 0.064 -1.188 -1.231 0.609 0.249 -0.414 0.4432791027 166 0.064 -1.188 -1.231 0.609 0.249 -0.406 0.4432686467 powell nthiter 2: fret = 0.443269 177 0.014 -1.188 -1.231 0.609 0.249 -0.406 0.4431417804 178 0.030 -1.188 -1.231 0.609 0.249 -0.406 0.4431205977 180 0.029 -1.188 -1.231 0.609 0.249 -0.406 0.4431205144 188 0.029 -1.153 -1.231 0.609 0.249 -0.406 0.4428255929 189 0.029 -1.140 -1.231 0.609 0.249 -0.406 0.4427954920 190 0.029 -1.137 -1.231 0.609 0.249 -0.406 0.4427940646 200 0.029 -1.137 -1.183 0.609 0.249 -0.406 0.4424758420 203 0.029 -1.137 -1.179 0.609 0.249 -0.406 0.4424577685 204 0.029 -1.137 -1.170 0.609 0.249 -0.406 0.4424411574 213 0.029 -1.137 -1.170 0.574 0.249 -0.406 0.4422697303 215 0.029 -1.137 -1.170 0.575 0.249 -0.406 0.4422690253 217 0.029 -1.137 -1.170 0.576 0.249 -0.406 0.4422686842 225 0.029 -1.137 -1.170 0.576 0.265 -0.406 0.4422097408 227 0.029 -1.137 -1.170 0.576 0.267 -0.406 0.4422076602 228 0.029 -1.137 -1.170 0.576 0.268 -0.406 0.4422075291 237 0.029 -1.137 -1.170 0.576 0.268 -0.410 0.4421993278 238 0.029 -1.137 -1.170 0.576 0.268 -0.415 0.4421972961 239 0.029 -1.137 -1.170 0.576 0.268 -0.414 0.4421958164 powell nthiter 3: fret = 0.442196 249 0.064 -1.137 -1.170 0.576 0.268 -0.414 0.4419168532 252 0.065 -1.137 -1.170 0.576 0.268 -0.414 0.4419163016 261 0.065 -1.109 -1.170 0.576 0.268 -0.414 0.4419152134 262 0.065 -1.122 -1.170 0.576 0.268 -0.414 0.4419009678 263 0.065 -1.123 -1.170 0.576 0.268 -0.414 0.4419006880 264 0.065 -1.125 -1.170 0.576 0.268 -0.414 0.4419004515 265 0.065 -1.129 -1.170 0.576 0.268 -0.414 0.4419001400 278 0.065 -1.129 -1.155 0.576 0.268 -0.414 0.4418149364 279 0.065 -1.129 -1.153 0.576 0.268 -0.414 0.4418140676 288 0.065 -1.129 -1.153 0.545 0.268 -0.414 0.4417746102 289 0.065 -1.129 -1.153 0.551 0.268 -0.414 0.4417693583 290 0.065 -1.129 -1.153 0.553 0.268 -0.414 0.4417673736 292 0.065 -1.129 -1.153 0.556 0.268 -0.414 0.4417671841 293 0.065 -1.129 -1.153 0.557 0.268 -0.414 0.4417671758 303 0.065 -1.129 -1.153 0.557 0.269 -0.414 0.4417654288 304 0.065 -1.129 -1.153 0.557 0.272 -0.414 0.4417624535 307 0.065 -1.129 -1.153 0.557 0.273 -0.414 0.4417624378 324 0.079 -1.127 -1.147 0.550 0.274 -0.414 0.4417397939 325 0.076 -1.127 -1.148 0.552 0.274 -0.414 0.4417387786 326 0.077 -1.127 -1.148 0.551 0.274 -0.414 0.4417378777 327 0.077 -1.127 -1.147 0.551 0.274 -0.414 0.4417377300 328 0.077 -1.127 -1.148 0.551 0.274 -0.414 0.4417375801 powell nthiter 4: fret = 0.441738 349 0.077 -1.065 -1.148 0.551 0.274 -0.414 0.4414113301 350 0.077 -1.068 -1.148 0.551 0.274 -0.414 0.4413576088 351 0.077 -1.089 -1.148 0.551 0.274 -0.414 0.4411795384 353 0.077 -1.088 -1.148 0.551 0.274 -0.414 0.4411787715 366 0.077 -1.088 -1.139 0.551 0.274 -0.414 0.4411445115 375 0.077 -1.088 -1.139 0.520 0.274 -0.414 0.4410480300 377 0.077 -1.088 -1.139 0.525 0.274 -0.414 0.4410398484 379 0.077 -1.088 -1.139 0.528 0.274 -0.414 0.4410391734 380 0.077 -1.088 -1.139 0.529 0.274 -0.414 0.4410390503 390 0.077 -1.088 -1.139 0.529 0.260 -0.414 0.4410009769 391 0.077 -1.088 -1.139 0.529 0.262 -0.414 0.4409993294 392 0.077 -1.088 -1.139 0.529 0.261 -0.414 0.4409987402 399 0.069 -1.089 -1.143 0.533 0.260 -0.414 0.4409480737 400 0.068 -1.089 -1.143 0.533 0.260 -0.414 0.4409469051 402 0.067 -1.090 -1.144 0.534 0.260 -0.414 0.4409453731 403 0.067 -1.090 -1.143 0.534 0.260 -0.414 0.4409451768 405 0.067 -1.090 -1.144 0.534 0.260 -0.414 0.4409449293 powell nthiter 5: fret = 0.440945 415 0.067 -1.090 -1.144 0.534 0.260 -0.399 0.4409404064 416 0.067 -1.090 -1.144 0.534 0.260 -0.405 0.4409364353 417 0.067 -1.090 -1.144 0.534 0.260 -0.404 0.4409364331 427 0.067 -1.087 -1.144 0.534 0.260 -0.404 0.4409361415 429 0.067 -1.088 -1.144 0.534 0.260 -0.404 0.4409355600 440 0.067 -1.088 -1.135 0.534 0.260 -0.404 0.4409198963 441 0.067 -1.088 -1.137 0.534 0.260 -0.404 0.4409196252 449 0.067 -1.088 -1.137 0.523 0.260 -0.404 0.4409122748 450 0.067 -1.088 -1.137 0.524 0.260 -0.404 0.4409112241 451 0.067 -1.088 -1.137 0.526 0.260 -0.404 0.4409107888 453 0.067 -1.088 -1.137 0.525 0.260 -0.404 0.4409106563 462 0.067 -1.088 -1.137 0.525 0.255 -0.404 0.4409105398 463 0.067 -1.088 -1.137 0.525 0.258 -0.404 0.4409098079 472 0.064 -1.089 -1.138 0.527 0.257 -0.404 0.4409013201 473 0.063 -1.089 -1.139 0.527 0.257 -0.404 0.4409001664 474 0.062 -1.089 -1.139 0.528 0.257 -0.404 0.4409001580 481 0.062 -1.089 -1.139 0.528 0.257 -0.404 0.4409000312 powell nthiter 6: fret = 0.440900 494 0.062 -1.089 -1.139 0.528 0.257 -0.408 0.4408995436 496 0.062 -1.089 -1.139 0.528 0.257 -0.406 0.4408991898 507 0.062 -1.087 -1.139 0.528 0.257 -0.406 0.4408974977 520 0.062 -1.087 -1.134 0.528 0.257 -0.406 0.4408942549 521 0.062 -1.087 -1.136 0.528 0.257 -0.406 0.4408939481 529 0.062 -1.087 -1.136 0.522 0.257 -0.406 0.4408930579 530 0.062 -1.087 -1.136 0.524 0.257 -0.406 0.4408920857 541 0.062 -1.087 -1.136 0.524 0.258 -0.406 0.4408911301 551 0.061 -1.087 -1.136 0.524 0.258 -0.406 0.4408908108 552 0.061 -1.087 -1.136 0.524 0.258 -0.406 0.4408901586 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 1.041597 1 -25.0 -25.0 25.0 1.069794 2 -25.0 25.0 -25.0 1.029993 3 -25.0 25.0 25.0 0.985568 4 25.0 -25.0 -25.0 1.028318 5 25.0 -25.0 25.0 0.993068 6 25.0 25.0 -25.0 1.019532 7 25.0 25.0 25.0 1.040036 REL: 8 0.440890 8.207906 1.025988 rel = 0.429722 Number of iterations 6 Min cost was 0.440890 Number of FunctionCalls 557 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.478072 sec Parameters at optimum (transmm) 0.06139 -1.08697 -1.13623 Parameters at optimum (rotdeg) 0.52411 0.25803 -0.40626 Final costs ---------------- Number of surface hits 2399 WM Intensity 9485.5101 +/- 1175.1985 Ctx Intensity 9972.6863 +/- 1537.6885 Pct Contrast 4.2517 +/- 16.5271 Cost 0.4409 RelCost 0.5896 Reg at min cost was 0.99999 0.00118 -0.00396 -3.59710; 0.00411 -0.39331 0.91940 -25.88477; 0.00048 0.91941 0.39331 15.56184; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/007/tmp.bbregister.76040/bbr.pass1.dat, type = 14 Original Reg 0.99993 -0.00017 -0.01225 -3.55773; 0.01124 -0.38486 0.92291 -24.66948; 0.00488 0.92297 0.38483 16.90858; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00007 -0.00135 -0.00829 0.03937; 0.00714 0.00844 0.00351 1.21529; 0.00440 0.00357 -0.00848 1.34674; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 1.387411 Computing change in rh position Surface-RMS-Diff-mm 1.574568 0.379784 2.440285 mri_segreg done mri_segreg --mov bold/007/tmp.bbregister.76040/template.nii --init-reg bold/007/tmp.bbregister.76040/bbr.pass1.dat --out-reg bold/007/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/007/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/007/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/007/tmp.bbregister.76040/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.4.1 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 mri_segreg --mov bold/007/tmp.bbregister.76040/template.nii --init-reg bold/007/tmp.bbregister.76040/bbr.pass1.dat --out-reg bold/007/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/007/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/007/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/007/tmp.bbregister.76040/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch movvol bold/007/tmp.bbregister.76040/template.nii regfile bold/007/tmp.bbregister.76040/bbr.pass1.dat subject 20231006_da047 dof 6 outregfile bold/007/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750319728 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99999 0.00118 -0.00396 -3.59710; 0.00411 -0.39331 0.91940 -25.88477; 0.00048 0.91941 0.39331 15.56184; 0.00000 0.00000 0.00000 1.00000; Loading mov INFO: This is an unsigined short. ExcludeZeroVoxels 1 Reading in targ vol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.029238 1 -25.0 -25.0 25.0 1.048318 2 -25.0 25.0 -25.0 1.026070 3 -25.0 25.0 25.0 1.014423 4 25.0 -25.0 -25.0 1.024474 5 25.0 -25.0 25.0 0.994385 6 25.0 25.0 -25.0 1.011222 7 25.0 25.0 25.0 1.027700 REL: 8 0.443827 8.175829 1.021979 rel = 0.434282 Initial costs ---------------- Number of surface hits 239836 WM Intensity 9477.5012 +/- 1157.4145 Ctx Intensity 9980.8973 +/- 1475.2237 Pct Contrast 4.5434 +/- 15.7848 Cost 0.4438 RelCost 0.4343 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.4485 0.4485 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.4474 0.4474 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.4457 0.4457 0.0 10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.4457 0.4457 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.4447 0.4447 0.0 18 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 -0.1000 0.4439 0.4439 0.0 19 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.0000 0.4436 0.4436 0.0 21 -0.1000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.4433 0.4433 0.0 22 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.0000 0.4433 0.4433 0.0 102 -0.1000 0.0000 -0.1000 0.1000 0.0000 -0.1000 0.4432 0.4432 0.0 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.4425 0.4425 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.4425 0.4425 0.0 355 0.0000 0.0000 0.0000 -0.1000 0.0000 0.0000 0.4423 0.4423 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.4419 0.4419 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.4409 0.4409 0.0 Brute Force -------------------------- Min cost was 0.440890 Number of iterations 729 Search time 0.612121 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.443827 7 0.096 0.000 0.000 0.000 0.000 0.000 0.4429854515 9 0.095 0.000 0.000 0.000 0.000 0.000 0.4429851419 17 0.095 -0.015 0.000 0.000 0.000 0.000 0.4429363100 18 0.095 -0.035 0.000 0.000 0.000 0.000 0.4429236262 19 0.095 -0.029 0.000 0.000 0.000 0.000 0.4429212437 28 0.095 -0.029 -0.281 0.000 0.000 0.000 0.4380844704 29 0.095 -0.029 -0.282 0.000 0.000 0.000 0.4380836669 30 0.095 -0.029 -0.289 0.000 0.000 0.000 0.4380816447 39 0.095 -0.029 -0.289 0.382 0.000 0.000 0.4379334446 40 0.095 -0.029 -0.289 0.195 0.000 0.000 0.4364551460 41 0.095 -0.029 -0.289 0.196 0.000 0.000 0.4364541887 42 0.095 -0.029 -0.289 0.206 0.000 0.000 0.4364491827 44 0.095 -0.029 -0.289 0.207 0.000 0.000 0.4364490129 45 0.095 -0.029 -0.289 0.209 0.000 0.000 0.4364487969 49 0.095 -0.029 -0.289 0.211 0.000 0.000 0.4364483446 58 0.095 -0.029 -0.289 0.211 0.012 0.000 0.4364089169 59 0.095 -0.029 -0.289 0.211 0.031 0.000 0.4363763570 61 0.095 -0.029 -0.289 0.211 0.037 0.000 0.4363742702 69 0.095 -0.029 -0.289 0.211 0.037 0.382 0.4360132718 70 0.095 -0.029 -0.289 0.211 0.037 0.205 0.4348660502 72 0.095 -0.029 -0.289 0.211 0.037 0.209 0.4348652829 74 0.095 -0.029 -0.289 0.211 0.037 0.210 0.4348650488 78 0.095 -0.029 -0.289 0.211 0.037 0.211 0.4348650347 powell nthiter 1: fret = 0.434865 87 0.140 -0.029 -0.289 0.211 0.037 0.211 0.4346469785 88 0.145 -0.029 -0.289 0.211 0.037 0.211 0.4346454013 97 0.144 -0.010 -0.289 0.211 0.037 0.211 0.4346152270 98 0.144 -0.008 -0.289 0.211 0.037 0.211 0.4346150734 100 0.144 -0.009 -0.289 0.211 0.037 0.211 0.4346149425 107 0.144 -0.009 -0.336 0.211 0.037 0.211 0.4343536699 108 0.144 -0.009 -0.363 0.211 0.037 0.211 0.4343290525 109 0.144 -0.009 -0.357 0.211 0.037 0.211 0.4343255655 110 0.144 -0.009 -0.356 0.211 0.037 0.211 0.4343255593 120 0.144 -0.009 -0.356 0.210 0.037 0.211 0.4343254710 129 0.144 -0.009 -0.356 0.210 0.026 0.211 0.4343152569 138 0.144 -0.009 -0.356 0.210 0.026 0.217 0.4343087252 139 0.144 -0.009 -0.356 0.210 0.026 0.228 0.4343060256 140 0.144 -0.009 -0.356 0.210 0.026 0.225 0.4343057961 141 0.144 -0.009 -0.356 0.210 0.026 0.226 0.4343056724 powell nthiter 2: fret = 0.434306 150 0.143 -0.009 -0.356 0.210 0.026 0.226 0.4343053937 158 0.143 -0.007 -0.356 0.210 0.026 0.226 0.4343047973 159 0.143 -0.005 -0.356 0.210 0.026 0.226 0.4343045377 186 0.143 -0.005 -0.357 0.210 0.025 0.226 0.4343045059 powell nthiter 3: fret = 0.434305 222 0.143 -0.005 -0.356 0.210 0.025 0.226 0.4343044754 powell nthiter 4: fret = 0.434304 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.029239 1 -25.0 -25.0 25.0 1.050751 2 -25.0 25.0 -25.0 1.023836 3 -25.0 25.0 25.0 1.013128 4 25.0 -25.0 -25.0 1.020455 5 25.0 -25.0 25.0 0.994368 6 25.0 25.0 -25.0 1.011477 7 25.0 25.0 25.0 1.030053 REL: 8 0.434304 8.173307 1.021663 rel = 0.425095 Number of iterations 4 Min cost was 0.434304 Number of FunctionCalls 305 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 13.530240 sec Parameters at optimum (transmm) 0.14294 -0.00536 -0.35555 Parameters at optimum (rotdeg) 0.20994 0.02482 0.22610 Final costs ---------------- Number of surface hits 239836 WM Intensity 9464.5529 +/- 1177.7793 Ctx Intensity 9972.2488 +/- 1518.4915 Pct Contrast 4.5324 +/- 16.6738 Cost 0.4343 RelCost 0.4343 Reg at min cost was 0.99997 0.00314 -0.00741 -3.34506; 0.00805 -0.39667 0.91793 -25.96094; 0.00006 0.91796 0.39668 15.11289; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/007/register.dof6.dat, type = 14 Original Reg 0.99999 0.00118 -0.00396 -3.59710; 0.00411 -0.39331 0.91940 -25.88477; 0.00048 0.91941 0.39331 15.56184; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00002 -0.00196 0.00345 -0.25204; -0.00394 0.00336 0.00147 0.07617; 0.00042 0.00145 -0.00337 0.44895; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.413795 Computing change in rh position Surface-RMS-Diff-mm 0.427963 0.120858 0.672154 mri_segreg done MinCost: 0.434304 9464.552909 9972.248846 4.532429 tkregister2_cmdl --mov bold/007/template.nii.gz --reg bold/007/register.dof6.dat --noedit --ltaout bold/007/register.dof6.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/007/template.nii.gz reg file bold/007/register.dof6.dat LoadVol 0 ZeroCRAS 0 7.4.1 Diagnostic Level -1 ---- Input registration matrix -------- 0.99997 0.00314 -0.00741 -3.34506; 0.00805 -0.39667 0.91793 -25.96094; 0.00006 0.91796 0.39668 15.11289; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: This is an unsigined short. INFO: loading target /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/007/template.nii.gz INFO: This is an unsigined short. Tmov: -------------------- -2.00000 0.00000 0.00000 110.00000; 0.00000 0.00000 2.00000 -60.00000; 0.00000 -2.00000 0.00000 110.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99997 0.00314 -0.00741 -3.34506; 0.00805 -0.39667 0.91793 -25.96094; 0.00006 0.91796 0.39668 15.11289; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = 20231006_da047 RegMat --------------------------- 0.99997 0.00314 -0.00741 -3.34506; 0.00805 -0.39667 0.91793 -25.96094; 0.00006 0.91796 0.39668 15.11289; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Wed Jun 18 10:12:10 EDT 2025 Ended at Wed Jun 18 10:13:04 EDT 2025 BBR-Run-Time-Sec 54 bbregister Done To check results, run: tkregisterfv --mov bold/007/template.nii.gz --reg bold/007/register.dof6.lta --surfs --sd /Volumes/umms-hillmera/asem_ptsd/DA047 Wed Jun 18 10:13:04 EDT 2025 register-sess completed 20231006_da047 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s 20231006_da047 -d /Volumes/umms-hillmera/asem_ptsd/DA047 -per-run -update ------------------------------------------------ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 Wed Jun 18 10:13:04 EDT 2025 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/register.dof6.lta -ndil 1 -nerode 0 Wed Jun 18 10:13:05 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold /Applications/freesurfer/fsfast/bin/mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/register.dof6.lta -ndil 1 -nerode 0 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_vol2vol --mov template.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/register.dof6.lta --inv --interp nearest --o masks/brain.nii.gz --targ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: -0.08631 0.99486 0.05288 0.78645; 0.99593 0.08478 0.03047 4.83148; -0.02583 -0.05529 0.99814 3.39664; 0.00000 0.00000 0.00000 1.00000; movvol template.nii.gz targvol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz outvol masks/brain.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750999144 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: -0.08631 0.99593 -0.02583 -4.65622; 0.99486 0.08478 -0.05529 -1.00423; 0.05288 0.03047 0.99814 -3.57911; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: -0.08631 -0.02583 -0.99593 234.65219; 0.05288 0.99814 -0.03047 -0.26900; -0.99486 0.05529 0.08478 239.80051; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i masks/brain.nii.gz --o masks/brain.nii.gz --min 0.5 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i masks/brain.nii.gz --o masks/brain.nii.gz --min 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 1096518 values in range Counting number of voxels in first frame Found 1096517 voxels in final mask Writing output to masks/brain.nii.gz Count: 1096517 1096517.000000 11534336 9.506546 mri_binarize done Diliating 1 mri_binarize --i masks/brain.nii.gz --min 0.5 --dilate 1 --o masks/brain.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i masks/brain.nii.gz --min 0.5 --dilate 1 --o masks/brain.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 1096518 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 1302459 voxels in final mask Writing output to masks/brain.nii.gz Count: 1302459 1302459.000000 11534336 11.292015 mri_binarize done Started at Wed Jun 18 10:13:05 EDT 2025 Ended at Wed Jun 18 10:13:09 EDT 2025 Mkbrainmask-Run-Time-Sec 4 mkbrainmask Done mri_binarize --i masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o masks/brain.e3.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o masks/brain.e3.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 1302460 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 892432 voxels in final mask Writing output to masks/brain.e3.nii.gz Count: 892432 892432.000000 11534336 7.737177 mri_binarize done mkbrainmask -i 002/template.nii.gz -o 002/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/register.dof6.lta -ndil 1 -nerode 0 Wed Jun 18 10:13:13 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold /Applications/freesurfer/fsfast/bin/mkbrainmask -i 002/template.nii.gz -o 002/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/register.dof6.lta -ndil 1 -nerode 0 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_vol2vol --mov 002/template.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/register.dof6.lta --inv --interp nearest --o 002/masks/brain.nii.gz --targ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: -0.08631 0.99486 0.05288 0.78645; 0.99593 0.08478 0.03047 4.83148; -0.02583 -0.05529 0.99814 3.39664; 0.00000 0.00000 0.00000 1.00000; movvol 002/template.nii.gz targvol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz outvol 002/masks/brain.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750888189 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: -0.08631 0.99593 -0.02583 -4.65622; 0.99486 0.08478 -0.05529 -1.00423; 0.05288 0.03047 0.99814 -3.57911; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: -0.08631 -0.02583 -0.99593 234.65219; 0.05288 0.99814 -0.03047 -0.26900; -0.99486 0.05529 0.08478 239.80051; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 002/masks/brain.nii.gz --o 002/masks/brain.nii.gz --min 0.5 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 002/masks/brain.nii.gz --o 002/masks/brain.nii.gz --min 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 002/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 002/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 1096518 values in range Counting number of voxels in first frame Found 1096517 voxels in final mask Writing output to 002/masks/brain.nii.gz Count: 1096517 1096517.000000 11534336 9.506546 mri_binarize done Diliating 1 mri_binarize --i 002/masks/brain.nii.gz --min 0.5 --dilate 1 --o 002/masks/brain.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 002/masks/brain.nii.gz --min 0.5 --dilate 1 --o 002/masks/brain.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 002/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 002/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 1096518 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 1302459 voxels in final mask Writing output to 002/masks/brain.nii.gz Count: 1302459 1302459.000000 11534336 11.292015 mri_binarize done Started at Wed Jun 18 10:13:13 EDT 2025 Ended at Wed Jun 18 10:13:16 EDT 2025 Mkbrainmask-Run-Time-Sec 3 mkbrainmask Done mri_binarize --i 002/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 002/masks/brain.e3.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 002/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 002/masks/brain.e3.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 002/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 002/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 1302460 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 892432 voxels in final mask Writing output to 002/masks/brain.e3.nii.gz Count: 892432 892432.000000 11534336 7.737177 mri_binarize done mkbrainmask -i 003/template.nii.gz -o 003/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/register.dof6.lta -ndil 1 -nerode 0 Wed Jun 18 10:13:22 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold /Applications/freesurfer/fsfast/bin/mkbrainmask -i 003/template.nii.gz -o 003/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/register.dof6.lta -ndil 1 -nerode 0 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_vol2vol --mov 003/template.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/register.dof6.lta --inv --interp nearest --o 003/masks/brain.nii.gz --targ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99999 -0.00092 -0.00521 -2.32047; 0.00448 -0.37481 0.92709 -25.45193; 0.00280 0.92710 0.37480 15.67991; 0.00000 0.00000 0.00000 1.00000; movvol 003/template.nii.gz targvol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz outvol 003/masks/brain.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750516256 Invert! INFO: This is an unsigined short. Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99999 0.00448 0.00280 2.39065; -0.00092 -0.37481 0.92710 -24.07865; -0.00521 0.92709 0.37480 17.70731; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 1.99997 0.00560 -0.00897 15.58973; -0.01041 0.74960 -1.85418 128.97110; 0.00183 -1.85420 -0.74962 229.78958; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 003/masks/brain.nii.gz --o 003/masks/brain.nii.gz --min 0.5 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 003/masks/brain.nii.gz --o 003/masks/brain.nii.gz --min 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 003/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 003/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 136878 values in range Counting number of voxels in first frame Found 136877 voxels in final mask Writing output to 003/masks/brain.nii.gz Count: 136877 1095016.000000 774400 17.675232 mri_binarize done Diliating 1 mri_binarize --i 003/masks/brain.nii.gz --min 0.5 --dilate 1 --o 003/masks/brain.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 003/masks/brain.nii.gz --min 0.5 --dilate 1 --o 003/masks/brain.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 003/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 003/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 136878 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 176959 voxels in final mask Writing output to 003/masks/brain.nii.gz Count: 176959 1415672.000000 774400 22.851111 mri_binarize done Started at Wed Jun 18 10:13:21 EDT 2025 Ended at Wed Jun 18 10:13:22 EDT 2025 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i 003/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 003/masks/brain.e3.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 003/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 003/masks/brain.e3.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 003/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 003/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 176327 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 101641 voxels in final mask Writing output to 003/masks/brain.e3.nii.gz Count: 101641 813128.000000 774400 13.125129 mri_binarize done mkbrainmask -i 004/template.nii.gz -o 004/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/register.dof6.lta -ndil 1 -nerode 0 Wed Jun 18 10:13:23 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold /Applications/freesurfer/fsfast/bin/mkbrainmask -i 004/template.nii.gz -o 004/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/register.dof6.lta -ndil 1 -nerode 0 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_vol2vol --mov 004/template.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/register.dof6.lta --inv --interp nearest --o 004/masks/brain.nii.gz --targ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99997 -0.00375 -0.00626 -2.32504; 0.00443 -0.36934 0.92928 -24.91978; 0.00580 0.92929 0.36931 15.51810; 0.00000 0.00000 0.00000 1.00000; movvol 004/template.nii.gz targvol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz outvol 004/masks/brain.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1751232761 Invert! INFO: This is an unsigined short. Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99997 0.00443 0.00580 2.34542; -0.00375 -0.36934 0.92929 -23.63338; -0.00626 0.92928 0.36931 17.41193; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 1.99995 0.01159 -0.00886 15.30347; -0.01251 0.73863 -1.85857 130.12578; 0.00750 -1.85857 -0.73868 229.81345; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 004/masks/brain.nii.gz --o 004/masks/brain.nii.gz --min 0.5 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 004/masks/brain.nii.gz --o 004/masks/brain.nii.gz --min 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 004/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 004/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 136947 values in range Counting number of voxels in first frame Found 136946 voxels in final mask Writing output to 004/masks/brain.nii.gz Count: 136946 1095568.000000 774400 17.684143 mri_binarize done Diliating 1 mri_binarize --i 004/masks/brain.nii.gz --min 0.5 --dilate 1 --o 004/masks/brain.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 004/masks/brain.nii.gz --min 0.5 --dilate 1 --o 004/masks/brain.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 004/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 004/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 136947 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 176972 voxels in final mask Writing output to 004/masks/brain.nii.gz Count: 176972 1415776.000000 774400 22.852789 mri_binarize done Started at Wed Jun 18 10:13:23 EDT 2025 Ended at Wed Jun 18 10:13:24 EDT 2025 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i 004/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 004/masks/brain.e3.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 004/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 004/masks/brain.e3.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 004/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 004/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 176351 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 101712 voxels in final mask Writing output to 004/masks/brain.e3.nii.gz Count: 101712 813696.000000 774400 13.134298 mri_binarize done mkbrainmask -i 005/template.nii.gz -o 005/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/register.dof6.lta -ndil 1 -nerode 0 Wed Jun 18 10:13:25 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold /Applications/freesurfer/fsfast/bin/mkbrainmask -i 005/template.nii.gz -o 005/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/register.dof6.lta -ndil 1 -nerode 0 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_vol2vol --mov 005/template.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/register.dof6.lta --inv --interp nearest --o 005/masks/brain.nii.gz --targ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99987 0.01413 -0.00825 -3.09594; 0.01295 -0.37459 0.92710 -23.94865; -0.01001 0.92708 0.37473 15.79257; 0.00000 0.00000 0.00000 1.00000; movvol 005/template.nii.gz targvol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz outvol 005/masks/brain.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750954359 Invert! INFO: This is an unsigined short. Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99987 0.01295 -0.01001 3.56357; 0.01413 -0.37459 0.92708 -23.56828; -0.00825 0.92710 0.37473 16.25933; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 1.99973 -0.02001 -0.02589 16.32851; -0.01651 0.74945 -1.85420 127.05457; -0.02826 -1.85416 -0.74919 230.44034; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 005/masks/brain.nii.gz --o 005/masks/brain.nii.gz --min 0.5 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 005/masks/brain.nii.gz --o 005/masks/brain.nii.gz --min 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 005/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 005/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 136418 values in range Counting number of voxels in first frame Found 136417 voxels in final mask Writing output to 005/masks/brain.nii.gz Count: 136417 1091336.000000 726000 18.790220 mri_binarize done Diliating 1 mri_binarize --i 005/masks/brain.nii.gz --min 0.5 --dilate 1 --o 005/masks/brain.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 005/masks/brain.nii.gz --min 0.5 --dilate 1 --o 005/masks/brain.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 005/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 005/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 136418 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 175929 voxels in final mask Writing output to 005/masks/brain.nii.gz Count: 175929 1407432.000000 726000 24.232645 mri_binarize done Started at Wed Jun 18 10:13:25 EDT 2025 Ended at Wed Jun 18 10:13:26 EDT 2025 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i 005/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 005/masks/brain.e3.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 005/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 005/masks/brain.e3.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 005/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 005/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 174911 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 100889 voxels in final mask Writing output to 005/masks/brain.e3.nii.gz Count: 100889 807112.000000 726000 13.896556 mri_binarize done mkbrainmask -i 006/template.nii.gz -o 006/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/register.dof6.lta -ndil 1 -nerode 0 Wed Jun 18 10:13:27 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold /Applications/freesurfer/fsfast/bin/mkbrainmask -i 006/template.nii.gz -o 006/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/register.dof6.lta -ndil 1 -nerode 0 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_vol2vol --mov 006/template.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/register.dof6.lta --inv --interp nearest --o 006/masks/brain.nii.gz --targ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99995 0.00876 -0.00542 -3.15799; 0.00845 -0.39667 0.91792 -26.00714; -0.00589 0.91792 0.39672 15.36434; 0.00000 0.00000 0.00000 1.00000; movvol 006/template.nii.gz targvol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz outvol 006/masks/brain.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750701377 Invert! INFO: This is an unsigined short. Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99995 0.00845 -0.00589 3.46809; 0.00876 -0.39667 0.91792 -24.39182; -0.00542 0.91792 0.39672 17.76003; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 1.99989 -0.01178 -0.01690 15.69268; -0.01084 0.79345 -1.83584 122.27206; -0.01752 -1.83584 -0.79334 229.34300; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 006/masks/brain.nii.gz --o 006/masks/brain.nii.gz --min 0.5 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 006/masks/brain.nii.gz --o 006/masks/brain.nii.gz --min 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 006/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 006/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 136317 values in range Counting number of voxels in first frame Found 136316 voxels in final mask Writing output to 006/masks/brain.nii.gz Count: 136316 1090528.000000 726000 18.776309 mri_binarize done Diliating 1 mri_binarize --i 006/masks/brain.nii.gz --min 0.5 --dilate 1 --o 006/masks/brain.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 006/masks/brain.nii.gz --min 0.5 --dilate 1 --o 006/masks/brain.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 006/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 006/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 136317 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 175869 voxels in final mask Writing output to 006/masks/brain.nii.gz Count: 175869 1406952.000000 726000 24.224380 mri_binarize done Started at Wed Jun 18 10:13:27 EDT 2025 Ended at Wed Jun 18 10:13:28 EDT 2025 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i 006/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 006/masks/brain.e3.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 006/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 006/masks/brain.e3.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 006/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 006/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 174984 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 101175 voxels in final mask Writing output to 006/masks/brain.e3.nii.gz Count: 101175 809400.000000 726000 13.935950 mri_binarize done mkbrainmask -i 007/template.nii.gz -o 007/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/007/register.dof6.lta -ndil 1 -nerode 0 Wed Jun 18 10:13:28 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold /Applications/freesurfer/fsfast/bin/mkbrainmask -i 007/template.nii.gz -o 007/masks/brain.nii.gz -reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/007/register.dof6.lta -ndil 1 -nerode 0 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 FreeSurferEnv.csh 7.4.1 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_vol2vol --mov 007/template.nii.gz --reg /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/007/register.dof6.lta --inv --interp nearest --o 007/masks/brain.nii.gz --targ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99997 0.00314 -0.00741 -3.34505; 0.00805 -0.39667 0.91793 -25.96094; 0.00006 0.91796 0.39668 15.11288; 0.00000 0.00000 0.00000 1.00000; movvol 007/template.nii.gz targvol /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/mri/aparc+aseg.mgz outvol 007/masks/brain.nii.gz regfile /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/007/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1750394088 Invert! INFO: This is an unsigined short. Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99997 0.00805 0.00006 3.55306; 0.00314 -0.39667 0.91796 -24.16029; -0.00741 0.91793 0.39668 17.81053; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 1.99994 0.00012 -0.01610 14.92717; -0.01482 0.79336 -1.83586 122.44592; -0.00628 -1.83592 -0.79333 228.96042; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 007/masks/brain.nii.gz --o 007/masks/brain.nii.gz --min 0.5 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 007/masks/brain.nii.gz --o 007/masks/brain.nii.gz --min 0.5 sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 007/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 007/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 136363 values in range Counting number of voxels in first frame Found 136362 voxels in final mask Writing output to 007/masks/brain.nii.gz Count: 136362 1090896.000000 726000 18.782645 mri_binarize done Diliating 1 mri_binarize --i 007/masks/brain.nii.gz --min 0.5 --dilate 1 --o 007/masks/brain.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 007/masks/brain.nii.gz --min 0.5 --dilate 1 --o 007/masks/brain.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 007/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 007/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 136363 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 175769 voxels in final mask Writing output to 007/masks/brain.nii.gz Count: 175769 1406152.000000 726000 24.210606 mri_binarize done Started at Wed Jun 18 10:13:28 EDT 2025 Ended at Wed Jun 18 10:13:29 EDT 2025 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i 007/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 007/masks/brain.e3.nii.gz 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_binarize --i 007/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 007/masks/brain.e3.nii.gz sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch input 007/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 007/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 174888 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 101207 voxels in final mask Writing output to 007/masks/brain.e3.nii.gz Count: 101207 809656.000000 726000 13.940358 mri_binarize done meanval --i 002/f.nii --m 002/masks/brain.e3.nii.gz --o 002/global.meanval.dat --avgwf 002/global.waveform.dat Wed Jun 18 10:13:31 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold /Applications/freesurfer/bin/meanval --i 002/f.nii --m 002/masks/brain.e3.nii.gz --o 002/global.meanval.dat --avgwf 002/global.waveform.dat freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_segstats --seg 002/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/tmpdir.meanval.77067/blah.77067 --in 002/f.nii --sfavg 002/global.meanval.dat --avgwf 002/global.waveform.dat 7.4.1 cwd cmdline mri_segstats --seg 002/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/tmpdir.meanval.77067/blah.77067 --in 002/f.nii --sfavg 002/global.meanval.dat --avgwf 002/global.waveform.dat sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch whitesurfname white UseRobust 0 Loading 002/masks/brain.e3.nii.gz Loading 002/f.nii Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to 002/global.meanval.dat 0 319.684 Writing to 002/global.waveform.dat mri_segstats done meanval --i 003/f.nii --m 003/masks/brain.e3.nii.gz --o 003/global.meanval.dat --avgwf 003/global.waveform.dat Wed Jun 18 10:13:34 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold /Applications/freesurfer/bin/meanval --i 003/f.nii --m 003/masks/brain.e3.nii.gz --o 003/global.meanval.dat --avgwf 003/global.waveform.dat freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_segstats --seg 003/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/tmpdir.meanval.77117/blah.77117 --in 003/f.nii --sfavg 003/global.meanval.dat --avgwf 003/global.waveform.dat 7.4.1 cwd cmdline mri_segstats --seg 003/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/tmpdir.meanval.77117/blah.77117 --in 003/f.nii --sfavg 003/global.meanval.dat --avgwf 003/global.waveform.dat sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch whitesurfname white UseRobust 0 Loading 003/masks/brain.e3.nii.gz Loading 003/f.nii INFO: This is an unsigined short. Voxel Volume is 8 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to 003/global.meanval.dat 0 1333.5 Writing to 003/global.waveform.dat mri_segstats done meanval --i 004/f.nii --m 004/masks/brain.e3.nii.gz --o 004/global.meanval.dat --avgwf 004/global.waveform.dat Wed Jun 18 10:13:37 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold /Applications/freesurfer/bin/meanval --i 004/f.nii --m 004/masks/brain.e3.nii.gz --o 004/global.meanval.dat --avgwf 004/global.waveform.dat freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_segstats --seg 004/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/tmpdir.meanval.77167/blah.77167 --in 004/f.nii --sfavg 004/global.meanval.dat --avgwf 004/global.waveform.dat 7.4.1 cwd cmdline mri_segstats --seg 004/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/tmpdir.meanval.77167/blah.77167 --in 004/f.nii --sfavg 004/global.meanval.dat --avgwf 004/global.waveform.dat sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch whitesurfname white UseRobust 0 Loading 004/masks/brain.e3.nii.gz Loading 004/f.nii INFO: This is an unsigined short. Voxel Volume is 8 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to 004/global.meanval.dat 0 1346.09 Writing to 004/global.waveform.dat mri_segstats done meanval --i 005/f.nii --m 005/masks/brain.e3.nii.gz --o 005/global.meanval.dat --avgwf 005/global.waveform.dat Wed Jun 18 10:13:40 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold /Applications/freesurfer/bin/meanval --i 005/f.nii --m 005/masks/brain.e3.nii.gz --o 005/global.meanval.dat --avgwf 005/global.waveform.dat freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_segstats --seg 005/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/tmpdir.meanval.77218/blah.77218 --in 005/f.nii --sfavg 005/global.meanval.dat --avgwf 005/global.waveform.dat 7.4.1 cwd cmdline mri_segstats --seg 005/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/tmpdir.meanval.77218/blah.77218 --in 005/f.nii --sfavg 005/global.meanval.dat --avgwf 005/global.waveform.dat sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch whitesurfname white UseRobust 0 Loading 005/masks/brain.e3.nii.gz Loading 005/f.nii INFO: This is an unsigined short. Voxel Volume is 8 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to 005/global.meanval.dat 0 10116.2 Writing to 005/global.waveform.dat mri_segstats done meanval --i 006/f.nii --m 006/masks/brain.e3.nii.gz --o 006/global.meanval.dat --avgwf 006/global.waveform.dat Wed Jun 18 10:14:05 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold /Applications/freesurfer/bin/meanval --i 006/f.nii --m 006/masks/brain.e3.nii.gz --o 006/global.meanval.dat --avgwf 006/global.waveform.dat freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_segstats --seg 006/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/tmpdir.meanval.77268/blah.77268 --in 006/f.nii --sfavg 006/global.meanval.dat --avgwf 006/global.waveform.dat 7.4.1 cwd cmdline mri_segstats --seg 006/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/006/tmpdir.meanval.77268/blah.77268 --in 006/f.nii --sfavg 006/global.meanval.dat --avgwf 006/global.waveform.dat sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch whitesurfname white UseRobust 0 Loading 006/masks/brain.e3.nii.gz Loading 006/f.nii INFO: This is an unsigined short. Voxel Volume is 8 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to 006/global.meanval.dat 0 9952.79 Writing to 006/global.waveform.dat mri_segstats done meanval --i 007/f.nii --m 007/masks/brain.e3.nii.gz --o 007/global.meanval.dat --avgwf 007/global.waveform.dat Wed Jun 18 10:14:32 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold /Applications/freesurfer/bin/meanval --i 007/f.nii --m 007/masks/brain.e3.nii.gz --o 007/global.meanval.dat --avgwf 007/global.waveform.dat freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_segstats --seg 007/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/007/tmpdir.meanval.77345/blah.77345 --in 007/f.nii --sfavg 007/global.meanval.dat --avgwf 007/global.waveform.dat 7.4.1 cwd cmdline mri_segstats --seg 007/masks/brain.e3.nii.gz --id 1 --sum /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/007/tmpdir.meanval.77345/blah.77345 --in 007/f.nii --sfavg 007/global.meanval.dat --avgwf 007/global.waveform.dat sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch whitesurfname white UseRobust 0 Loading 007/masks/brain.e3.nii.gz Loading 007/f.nii INFO: This is an unsigined short. Voxel Volume is 8 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to 007/global.meanval.dat 0 10069.7 Writing to 007/global.waveform.dat mri_segstats done Wed Jun 18 10:14:39 EDT 2025 mkbrainmask-sess done 20231006_da047 MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s 20231006_da047 -d /Volumes/umms-hillmera/asem_ptsd/DA047 -fsd bold -per-run -update Logfile is /Volumes/umms-hillmera/asem_ptsd/DA047/log/mc-20231006_da047-bold.log ------------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 RunList: 002 003 004 005 006 007 ------- ************************** ----------- ------- Motion Correcting Run 002 ----------- ------- ************************** ----------- sess = 20231006_da047 Wed Jun 18 10:14:39 EDT 2025 mc-afni2 --i 002/f.nii --t 002/template.nii.gz --o 002/fmcpr.nii.gz --mcdat 002/fmcpr.mcdat /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_info --nframes --o /tmp/mriinfo.77505 002/template.nii.gz log file is 002/fmcpr.nii.gz.mclog mcdat file is 002/fmcpr.mcdat tmp dir is 002/tmp.mc-afni2.77505 #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_convert 002/template.nii.gz 002/tmp.mc-afni2.77505/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 002/template.nii.gz 002/tmp.mc-afni2.77505/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 reading from 002/template.nii.gz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) changing data type from short to float (noscale = 0)... writing to 002/tmp.mc-afni2.77505/tempvol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_convert 002/f.nii 002/tmp.mc-afni2.77505/invol.nii.gz -odt float mri_convert 002/f.nii 002/tmp.mc-afni2.77505/invol.nii.gz -odt float reading from 002/f.nii... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) changing data type from short to float (noscale = 0)... writing to 002/tmp.mc-afni2.77505/invol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold 3dvolreg.afni -verbose -dfile 002/fmcpr.mcdat -1Dmatrix_save 002/fmcpr.mat -base 002/tmp.mc-afni2.77505/tempvol.nii.gz -prefix 002/tmp.mc-afni2.77505/outvol.nii.gz 002/tmp.mc-afni2.77505/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (May 22 2013) [64-bit] ++ Authored by: RW Cox ++ Reading in base dataset 002/tmp.mc-afni2.77505/tempvol.nii.gz ++ Reading input dataset 002/tmp.mc-afni2.77505/invol.nii.gz ++ Edging: x=13 y=13 z=9 ++ Creating mask for -maxdisp + Automask has 4279087 voxels + 124829 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 1 sub-bricks: 0.. ++ CPU time for realignment=0.1 s ++ Min : roll=-0.000 pitch=-0.000 yaw=-0.000 dS=+0.000 dL=-0.000 dP=+0.000 ++ Mean: roll=-0.000 pitch=-0.000 yaw=-0.000 dS=+0.000 dL=-0.000 dP=+0.000 ++ Max : roll=-0.000 pitch=-0.000 yaw=-0.000 dS=+0.000 dL=-0.000 dP=+0.000 ++ Max displacements (mm) for each sub-brick: 0.00 ++ Max displacement in automask = 0.00 (mm) at sub-brick 0 ++ Wrote dataset to disk in 002/tmp.mc-afni2.77505/outvol.nii.gz #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_convert 002/tmp.mc-afni2.77505/outvol.nii.gz 002/fmcpr.nii.gz --in_like 002/template.nii.gz mri_convert 002/tmp.mc-afni2.77505/outvol.nii.gz 002/fmcpr.nii.gz --in_like 002/template.nii.gz reading info from 002/template.nii.gz... reading from 002/tmp.mc-afni2.77505/outvol.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to 002/fmcpr.nii.gz... ... cleaning up .... Wed Jun 18 10:14:59 EDT 2025 mc-afni2 done INFO: Making external regressor from mc params mcdat2mcextreg --i 002/fmcpr.mcdat --o 002/mcprextreg Wed Jun 18 10:15:00 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold /Applications/freesurfer/fsfast/bin/mcdat2mcextreg --i 002/fmcpr.mcdat --o 002/mcprextreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/tmpdir.mcdat2extreg.77606/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/tmpdir.mcdat2extreg.77606/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/tmpdir.mcdat2extreg.77606/y.out.nii --pca 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/tmpdir.mcdat2extreg.77606/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/tmpdir.mcdat2extreg.77606/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/tmpdir.mcdat2extreg.77606/y.out.nii --pca sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/tmpdir.mcdat2extreg.77606/table.dat logyflag 0 usedti 0 glmdir /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/tmpdir.mcdat2extreg.77606/glm IllCondOK 0 ReScaleX 1 DoFFx 0 SigUseDouble 1 Creating output directory /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/tmpdir.mcdat2extreg.77606/glm Loading y from /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/tmpdir.mcdat2extreg.77606/table.dat Found 6 data colums Found 1 data rows Saving design matrix to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/002/tmpdir.mcdat2extreg.77606/glm/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 0 ERROR: DOF = 0 (base) hibahmch@mac-mvqmt7cvdq DA047 % preproc-sess -s 20231006_da047 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.20231006_da047.log -------------------------------------------------------------- FreeSurferEnv.csh 7.4.1 hibahmch setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 /Volumes/umms-hillmera/asem_ptsd/DA047 /Applications/freesurfer/fsfast/bin/preproc-sess -s 20231006_da047 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Wed Jun 18 10:15:07 EDT 2025 instem f mc 1 f fmcpr stc 1 fmcpr fmcpr.up sm 0 mask 1 brain 20231006_da047 Template ----------------------------- mktemplate-sess -s 20231006_da047 -d /Volumes/umms-hillmera/asem_ptsd/DA047 -fsd bold -funcstem f -update Session: /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 ---------------- Wed Jun 18 10:15:07 EDT 2025 Detected input format at nii 20231006_da047 Update not needed Run: 002 ---------------- Wed Jun 18 10:15:07 EDT 2025 20231006_da047 002 Update not needed Run: 003 ---------------- Wed Jun 18 10:15:08 EDT 2025 20231006_da047 003 Update not needed Run: 004 ---------------- Wed Jun 18 10:15:08 EDT 2025 20231006_da047 004 Update not needed Run: 005 ---------------- Wed Jun 18 10:15:08 EDT 2025 20231006_da047 005 Update not needed Run: 006 ---------------- Wed Jun 18 10:15:08 EDT 2025 20231006_da047 006 Update not needed Run: 007 ---------------- Wed Jun 18 10:15:08 EDT 2025 20231006_da047 007 Update not needed Wed Jun 18 10:15:08 EDT 2025 mktemplate-sess completed 20231006_da047 Registration ----------------------------- register-sess -s 20231006_da047 -d /Volumes/umms-hillmera/asem_ptsd/DA047 -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg -------------------------------------------------------------- register-sess logfile is /Volumes/umms-hillmera/asem_ptsd/DA047/log/register-sess.20231006_da047.log -------------------------------------------------------------- Wed Jun 18 10:15:09 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047 /Applications/freesurfer/fsfast/bin/register-sess -s 20231006_da047 -d /Volumes/umms-hillmera/asem_ptsd/DA047 -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 Session: /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 ---------------- Wed Jun 18 10:15:09 EDT 2025 /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 Run: 002 ---------------- Wed Jun 18 10:15:09 EDT 2025 Update not needed Run: 003 ---------------- Wed Jun 18 10:15:09 EDT 2025 Update not needed Run: 004 ---------------- Wed Jun 18 10:15:09 EDT 2025 Update not needed Run: 005 ---------------- Wed Jun 18 10:15:09 EDT 2025 Update not needed Run: 006 ---------------- Wed Jun 18 10:15:09 EDT 2025 Update not needed Run: 007 ---------------- Wed Jun 18 10:15:09 EDT 2025 Update not needed Wed Jun 18 10:15:10 EDT 2025 register-sess completed 20231006_da047 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s 20231006_da047 -d /Volumes/umms-hillmera/asem_ptsd/DA047 -per-run -update ------------------------------------------------ /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 Wed Jun 18 10:15:10 EDT 2025 20231006_da047 Update not needed for session-level mask 20231006_da047 Update not needed for run 002 mask 20231006_da047 Update not needed for run 003 mask 20231006_da047 Update not needed for run 004 mask 20231006_da047 Update not needed for run 005 mask 20231006_da047 Update not needed for run 006 mask 20231006_da047 Update not needed for run 007 mask 20231006_da047 Update not needed for run 002 meanval 20231006_da047 Update not needed for run 003 meanval 20231006_da047 Update not needed for run 004 meanval 20231006_da047 Update not needed for run 005 meanval 20231006_da047 Update not needed for run 006 meanval 20231006_da047 Update not needed for run 007 meanval Wed Jun 18 10:15:11 EDT 2025 mkbrainmask-sess done 20231006_da047 MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s 20231006_da047 -d /Volumes/umms-hillmera/asem_ptsd/DA047 -fsd bold -per-run -update Logfile is /Volumes/umms-hillmera/asem_ptsd/DA047/log/mc-20231006_da047-bold.log ------------------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047 RunList: 002 003 004 005 006 007 20231006_da047 002 Update not needed ------- ************************** ----------- ------- Motion Correcting Run 003 ----------- ------- ************************** ----------- sess = 20231006_da047 Wed Jun 18 10:15:12 EDT 2025 mc-afni2 --i 003/f.nii --t 003/template.nii.gz --o 003/fmcpr.nii.gz --mcdat 003/fmcpr.mcdat /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_info --nframes --o /tmp/mriinfo.78389 003/template.nii.gz INFO: This is an unsigined short. log file is 003/fmcpr.nii.gz.mclog mcdat file is 003/fmcpr.mcdat tmp dir is 003/tmp.mc-afni2.78389 #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_convert 003/template.nii.gz 003/tmp.mc-afni2.78389/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 003/template.nii.gz 003/tmp.mc-afni2.78389/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 reading from 003/template.nii.gz... INFO: This is an unsigined short. TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) changing data type from ushrt to float (noscale = 0)... writing to 003/tmp.mc-afni2.78389/tempvol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_convert 003/f.nii 003/tmp.mc-afni2.78389/invol.nii.gz -odt float mri_convert 003/f.nii 003/tmp.mc-afni2.78389/invol.nii.gz -odt float reading from 003/f.nii... INFO: This is an unsigined short. TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) changing data type from ushrt to float (noscale = 0)... writing to 003/tmp.mc-afni2.78389/invol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold 3dvolreg.afni -verbose -dfile 003/fmcpr.mcdat -1Dmatrix_save 003/fmcpr.mat -base 003/tmp.mc-afni2.78389/tempvol.nii.gz -prefix 003/tmp.mc-afni2.78389/outvol.nii.gz 003/tmp.mc-afni2.78389/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (May 22 2013) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 003/tmp.mc-afni2.78389/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:003/tmp.mc-afni2.78389/tempvol.nii.gz is 23.599995 degrees from plumb. ++ Reading in base dataset 003/tmp.mc-afni2.78389/tempvol.nii.gz ++ Oblique dataset:003/tmp.mc-afni2.78389/invol.nii.gz is 23.599995 degrees from plumb. ++ Reading input dataset 003/tmp.mc-afni2.78389/invol.nii.gz ++ Edging: x=6 y=6 z=3 ++ Creating mask for -maxdisp + Automask has 764962 voxels + 50630 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 65 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64.. ++ CPU time for realignment=4.33 s [=0.0666 s/sub-brick] ++ Min : roll=-0.144 pitch=-0.380 yaw=-0.640 dS=-3.596 dL=-0.110 dP=-0.259 ++ Mean: roll=-0.034 pitch=-0.032 yaw=+0.021 dS=-0.028 dL=-0.003 dP=+0.135 ++ Max : roll=+0.273 pitch=+0.184 yaw=+0.139 dS=+0.189 dL=+0.102 dP=+1.300 ++ Max displacements (mm) for each sub-brick: 5.80 0.37 0.20 0.31 0.55 0.36 0.30 0.47 0.17 0.24 0.39 0.36 0.31 0.14 0.18 0.19 0.20 0.62 0.15 0.27 0.30 0.36 0.26 0.51 0.63 0.63 0.36 0.55 0.56 0.67 0.30 0.17 0.00 0.54 0.22 0.38 0.46 0.76 0.56 0.60 0.35 0.64 0.42 0.37 0.25 0.26 0.19 0.22 0.70 0.45 0.79 0.45 0.94 0.59 0.61 0.84 0.42 0.50 0.80 0.75 0.46 1.01 0.81 0.88 0.64 ++ Max displacement in automask = 5.80 (mm) at sub-brick 0 ++ Wrote dataset to disk in 003/tmp.mc-afni2.78389/outvol.nii.gz #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_convert 003/tmp.mc-afni2.78389/outvol.nii.gz 003/fmcpr.nii.gz --in_like 003/template.nii.gz mri_convert 003/tmp.mc-afni2.78389/outvol.nii.gz 003/fmcpr.nii.gz --in_like 003/template.nii.gz reading info from 003/template.nii.gz... INFO: This is an unsigined short. reading from 003/tmp.mc-afni2.78389/outvol.nii.gz... TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 INFO: frames are not the same i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) writing to 003/fmcpr.nii.gz... ... cleaning up .... Wed Jun 18 10:15:56 EDT 2025 mc-afni2 done INFO: Making external regressor from mc params mcdat2mcextreg --i 003/fmcpr.mcdat --o 003/mcprextreg Wed Jun 18 10:15:56 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold /Applications/freesurfer/fsfast/bin/mcdat2mcextreg --i 003/fmcpr.mcdat --o 003/mcprextreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/tmpdir.mcdat2extreg.78504/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/tmpdir.mcdat2extreg.78504/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/tmpdir.mcdat2extreg.78504/y.out.nii --pca 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/tmpdir.mcdat2extreg.78504/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/tmpdir.mcdat2extreg.78504/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/tmpdir.mcdat2extreg.78504/y.out.nii --pca sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/tmpdir.mcdat2extreg.78504/table.dat logyflag 0 usedti 0 glmdir /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/tmpdir.mcdat2extreg.78504/glm IllCondOK 0 ReScaleX 1 DoFFx 0 SigUseDouble 1 Creating output directory /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/tmpdir.mcdat2extreg.78504/glm Loading y from /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/tmpdir.mcdat2extreg.78504/table.dat Found 6 data colums Found 65 data rows Saving design matrix to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/tmpdir.mcdat2extreg.78504/glm/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 64 Starting fit and test Fit completed in 1.66667e-05 minutes Writing results osgm maxvox sig=6.06166 F=29.6817 at index 5 0 0 seed=1750323865 Computing efficiency Measure:MC osgm Tx 5.680 Ty 1.930 Tz 1.077 Rx 0.206 Ry 0.200 Rz 6.062 Computing PCA (65) mri_glmfit done ninputs = 1 Checking inputs nframestot = 65 Allocing output Done allocing nframes = 65 Computing PCA Writing to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/003/tmpdir.mcdat2extreg.78504/pca.nii mcdat2mcextreg done ------- ************************** ----------- ------- Motion Correcting Run 004 ----------- ------- ************************** ----------- sess = 20231006_da047 Wed Jun 18 10:15:58 EDT 2025 mc-afni2 --i 004/f.nii --t 004/template.nii.gz --o 004/fmcpr.nii.gz --mcdat 004/fmcpr.mcdat /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_info --nframes --o /tmp/mriinfo.78568 004/template.nii.gz INFO: This is an unsigined short. log file is 004/fmcpr.nii.gz.mclog mcdat file is 004/fmcpr.mcdat tmp dir is 004/tmp.mc-afni2.78568 #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_convert 004/template.nii.gz 004/tmp.mc-afni2.78568/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 004/template.nii.gz 004/tmp.mc-afni2.78568/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 reading from 004/template.nii.gz... INFO: This is an unsigined short. TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) changing data type from ushrt to float (noscale = 0)... writing to 004/tmp.mc-afni2.78568/tempvol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_convert 004/f.nii 004/tmp.mc-afni2.78568/invol.nii.gz -odt float mri_convert 004/f.nii 004/tmp.mc-afni2.78568/invol.nii.gz -odt float reading from 004/f.nii... INFO: This is an unsigined short. TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) changing data type from ushrt to float (noscale = 0)... writing to 004/tmp.mc-afni2.78568/invol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save 004/fmcpr.mat -base 004/tmp.mc-afni2.78568/tempvol.nii.gz -prefix 004/tmp.mc-afni2.78568/outvol.nii.gz 004/tmp.mc-afni2.78568/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (May 22 2013) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 004/tmp.mc-afni2.78568/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:004/tmp.mc-afni2.78568/tempvol.nii.gz is 23.599995 degrees from plumb. ++ Reading in base dataset 004/tmp.mc-afni2.78568/tempvol.nii.gz ++ Oblique dataset:004/tmp.mc-afni2.78568/invol.nii.gz is 23.599995 degrees from plumb. ++ Reading input dataset 004/tmp.mc-afni2.78568/invol.nii.gz ++ Edging: x=6 y=6 z=3 ++ Creating mask for -maxdisp + Automask has 764962 voxels + 50630 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 65 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64.. ++ CPU time for realignment=4.57 s [=0.0703 s/sub-brick] ++ Min : roll=-0.061 pitch=-0.225 yaw=-0.743 dS=-3.657 dL=-0.173 dP=-0.115 ++ Mean: roll=+0.040 pitch=+0.095 yaw=-0.058 dS=-0.199 dL=-0.050 dP=+0.090 ++ Max : roll=+0.303 pitch=+0.675 yaw=+0.063 dS=+0.131 dL=+0.060 dP=+1.204 ++ Max displacements (mm) for each sub-brick: 5.76 0.64 0.66 0.45 0.65 0.54 0.53 0.36 0.47 0.34 0.43 0.45 0.47 0.42 0.40 0.32 0.26 0.37 0.41 0.26 0.30 0.05 0.21 0.28 0.12 0.24 0.14 0.26 0.14 0.09 0.18 0.20 0.00 0.96 0.85 2.47 1.43 1.27 1.13 0.93 1.07 0.98 0.93 0.98 0.89 0.77 0.68 0.71 0.79 0.66 0.61 0.68 0.55 0.64 0.78 0.61 0.72 0.47 0.59 0.52 0.57 0.64 0.63 0.49 0.53 ++ Max displacement in automask = 5.76 (mm) at sub-brick 0 ++ Wrote dataset to disk in 004/tmp.mc-afni2.78568/outvol.nii.gz #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_convert 004/tmp.mc-afni2.78568/outvol.nii.gz 004/fmcpr.nii.gz --in_like 004/template.nii.gz mri_convert 004/tmp.mc-afni2.78568/outvol.nii.gz 004/fmcpr.nii.gz --in_like 004/template.nii.gz reading info from 004/template.nii.gz... INFO: This is an unsigined short. reading from 004/tmp.mc-afni2.78568/outvol.nii.gz... TR=2369.00, TE=0.00, TI=0.00, flip angle=0.00 INFO: frames are not the same i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) writing to 004/fmcpr.nii.gz... ... cleaning up .... Wed Jun 18 10:16:54 EDT 2025 mc-afni2 done INFO: Making external regressor from mc params mcdat2mcextreg --i 004/fmcpr.mcdat --o 004/mcprextreg Wed Jun 18 10:16:54 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold /Applications/freesurfer/fsfast/bin/mcdat2mcextreg --i 004/fmcpr.mcdat --o 004/mcprextreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/tmpdir.mcdat2extreg.78673/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/tmpdir.mcdat2extreg.78673/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/tmpdir.mcdat2extreg.78673/y.out.nii --pca 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/tmpdir.mcdat2extreg.78673/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/tmpdir.mcdat2extreg.78673/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/tmpdir.mcdat2extreg.78673/y.out.nii --pca sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/tmpdir.mcdat2extreg.78673/table.dat logyflag 0 usedti 0 glmdir /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/tmpdir.mcdat2extreg.78673/glm IllCondOK 0 ReScaleX 1 DoFFx 0 SigUseDouble 1 Creating output directory /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/tmpdir.mcdat2extreg.78673/glm Loading y from /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/tmpdir.mcdat2extreg.78673/table.dat Found 6 data colums Found 65 data rows Saving design matrix to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/tmpdir.mcdat2extreg.78673/glm/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 64 Starting fit and test Fit completed in 0 minutes Writing results osgm maxvox sig=-8.71912 F=48.9103 at index 4 0 0 seed=1751164854 Computing efficiency Measure:MC osgm Tx 7.496 Ty 7.840 Tz 3.965 Rx 3.018 Ry 8.719 Rz 4.380 Computing PCA (65) mri_glmfit done ninputs = 1 Checking inputs nframestot = 65 Allocing output Done allocing nframes = 65 Computing PCA Writing to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/004/tmpdir.mcdat2extreg.78673/pca.nii mcdat2mcextreg done ------- ************************** ----------- ------- Motion Correcting Run 005 ----------- ------- ************************** ----------- sess = 20231006_da047 Wed Jun 18 10:16:55 EDT 2025 mc-afni2 --i 005/f.nii --t 005/template.nii.gz --o 005/fmcpr.nii.gz --mcdat 005/fmcpr.mcdat /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_info --nframes --o /tmp/mriinfo.78737 005/template.nii.gz INFO: This is an unsigined short. log file is 005/fmcpr.nii.gz.mclog mcdat file is 005/fmcpr.mcdat tmp dir is 005/tmp.mc-afni2.78737 #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_convert 005/template.nii.gz 005/tmp.mc-afni2.78737/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 005/template.nii.gz 005/tmp.mc-afni2.78737/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 reading from 005/template.nii.gz... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) changing data type from ushrt to float (noscale = 0)... writing to 005/tmp.mc-afni2.78737/tempvol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_convert 005/f.nii 005/tmp.mc-afni2.78737/invol.nii.gz -odt float mri_convert 005/f.nii 005/tmp.mc-afni2.78737/invol.nii.gz -odt float reading from 005/f.nii... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) changing data type from ushrt to float (noscale = 0)... writing to 005/tmp.mc-afni2.78737/invol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold 3dvolreg.afni -verbose -dfile 005/fmcpr.mcdat -1Dmatrix_save 005/fmcpr.mat -base 005/tmp.mc-afni2.78737/tempvol.nii.gz -prefix 005/tmp.mc-afni2.78737/outvol.nii.gz 005/tmp.mc-afni2.78737/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (May 22 2013) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 005/tmp.mc-afni2.78737/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:005/tmp.mc-afni2.78737/tempvol.nii.gz is 23.599995 degrees from plumb. ++ Reading in base dataset 005/tmp.mc-afni2.78737/tempvol.nii.gz ++ Oblique dataset:005/tmp.mc-afni2.78737/invol.nii.gz is 23.599995 degrees from plumb. ++ Reading input dataset 005/tmp.mc-afni2.78737/invol.nii.gz ++ Edging: x=6 y=6 z=3 ++ Creating mask for -maxdisp + Automask has 172971 voxels + 15653 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 100 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99.. ++ CPU time for realignment=4.72 s [=0.0472 s/sub-brick] ++ Min : roll=-0.061 pitch=-0.225 yaw=-0.071 dS=-0.051 dL=-0.044 dP=-0.084 ++ Mean: roll=+0.003 pitch=-0.109 yaw=+0.036 dS=+0.037 dL=+0.011 dP=+0.007 ++ Max : roll=+0.077 pitch=+0.000 yaw=+0.110 dS=+0.168 dL=+0.036 dP=+0.130 ++ Max displacements (mm) for each sub-brick: 0.24 0.22 0.12 0.11 0.15 0.16 0.17 0.12 0.13 0.14 0.16 0.17 0.16 0.14 0.20 0.16 0.16 0.14 0.17 0.19 0.19 0.17 0.26 0.20 0.20 0.17 0.21 0.22 0.18 0.17 0.26 0.21 0.19 0.18 0.24 0.21 0.15 0.15 0.26 0.23 0.20 0.28 0.32 0.21 0.25 0.34 0.24 0.25 0.36 0.13 0.00 0.12 0.08 0.23 0.12 0.11 0.14 0.25 0.14 0.13 0.27 0.23 0.20 0.25 0.33 0.23 0.24 0.35 0.24 0.25 0.38 0.21 0.15 0.16 0.16 0.20 0.21 0.19 0.21 0.34 0.21 0.25 0.36 0.31 0.30 0.31 0.35 0.28 0.34 0.48 0.30 0.29 0.33 0.47 0.34 0.37 0.48 0.25 0.21 0.24 ++ Max displacement in automask = 0.48 (mm) at sub-brick 96 ++ Wrote dataset to disk in 005/tmp.mc-afni2.78737/outvol.nii.gz #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_convert 005/tmp.mc-afni2.78737/outvol.nii.gz 005/fmcpr.nii.gz --in_like 005/template.nii.gz mri_convert 005/tmp.mc-afni2.78737/outvol.nii.gz 005/fmcpr.nii.gz --in_like 005/template.nii.gz reading info from 005/template.nii.gz... INFO: This is an unsigined short. reading from 005/tmp.mc-afni2.78737/outvol.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 INFO: frames are not the same i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) writing to 005/fmcpr.nii.gz... ... cleaning up .... Wed Jun 18 10:19:06 EDT 2025 mc-afni2 done INFO: Making external regressor from mc params mcdat2mcextreg --i 005/fmcpr.mcdat --o 005/mcprextreg Wed Jun 18 10:19:07 EDT 2025 setenv SUBJECTS_DIR /Volumes/umms-hillmera/asem_ptsd/DA047 cd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold /Applications/freesurfer/fsfast/bin/mcdat2mcextreg --i 005/fmcpr.mcdat --o 005/mcprextreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin mac-mvqmt7cvdq.ddns.med.umich.edu 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132 arm64 mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/tmpdir.mcdat2extreg.78844/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/tmpdir.mcdat2extreg.78844/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/tmpdir.mcdat2extreg.78844/y.out.nii --pca 7.4.1 cwd /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold cmdline mri_glmfit --table /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/tmpdir.mcdat2extreg.78844/table.dat --glmdir /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/tmpdir.mcdat2extreg.78844/glm --osgm --y-out /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/tmpdir.mcdat2extreg.78844/y.out.nii --pca sysname Darwin hostname mac-mvqmt7cvdq.ddns.med.umich.edu machine x86_64 user hibahmch FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/tmpdir.mcdat2extreg.78844/table.dat logyflag 0 usedti 0 glmdir /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/tmpdir.mcdat2extreg.78844/glm IllCondOK 0 ReScaleX 1 DoFFx 0 SigUseDouble 1 Creating output directory /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/tmpdir.mcdat2extreg.78844/glm Loading y from /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/tmpdir.mcdat2extreg.78844/table.dat Found 6 data colums Found 100 data rows Saving design matrix to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/tmpdir.mcdat2extreg.78844/glm/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 99 Starting fit and test Fit completed in 0 minutes Writing results osgm maxvox sig=-47.4326 F=756.531 at index 1 0 0 seed=1750637406 Computing efficiency Measure:MC osgm Tx 0.528 Ty 47.433 Tz 20.674 Rx 12.565 Ry 12.198 Rz 1.433 Computing PCA (100) mri_glmfit done ninputs = 1 Checking inputs nframestot = 100 Allocing output Done allocing nframes = 100 Computing PCA Writing to /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold/005/tmpdir.mcdat2extreg.78844/pca.nii mcdat2mcextreg done ------- ************************** ----------- ------- Motion Correcting Run 006 ----------- ------- ************************** ----------- sess = 20231006_da047 Wed Jun 18 10:19:08 EDT 2025 mc-afni2 --i 006/f.nii --t 006/template.nii.gz --o 006/fmcpr.nii.gz --mcdat 006/fmcpr.mcdat /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_info --nframes --o /tmp/mriinfo.78908 006/template.nii.gz INFO: This is an unsigined short. log file is 006/fmcpr.nii.gz.mclog mcdat file is 006/fmcpr.mcdat tmp dir is 006/tmp.mc-afni2.78908 #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_convert 006/template.nii.gz 006/tmp.mc-afni2.78908/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 006/template.nii.gz 006/tmp.mc-afni2.78908/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 reading from 006/template.nii.gz... INFO: This is an unsigined short. TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.916363, -0.400349) k_ras = (-0, -0.400349, 0.916363) changing data type from ushrt to float (noscale = 0)... writing to 006/tmp.mc-afni2.78908/tempvol.nii.gz... #@# -------------------------------- /Volumes/umms-hillmera/asem_ptsd/DA047/20231006_da047/bold mri_convert 006/f.nii 006/tmp.mc-afni2.78908/invol.nii.gz -odt float mri_convert 006/f.nii 006/tmp.mc-afni2.78908/invol.nii.gz -odt float