Fri Jul 29 12:28:42 CDT 2022 /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep /Applications/freesurfer/7.3.0/bin/trac-all -prep -c /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/config/tracula_config.txt -noqa Subject sub-0003107 SUBJECTS_DIR /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep FREESURFER_HOME /Applications/freesurfer/7.3.0 Actual FREESURFER_HOME /Applications/freesurfer/7.3.0 build-stamp.txt: freesurfer-darwin-macOS-7.3.0-20220717-7725d89 mbm3668 PSYC-A30765 Darwin PSYC-A30765 21.6.0 Darwin Kernel Version 21.6.0: Sat Jun 18 17:07:25 PDT 2022; root:xnu-8020.140.41~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 11136 PhysMem: 37G used (13G wired), 92G unused. ######################################## Program versions: FreeSurferEnv.csh 7.3.0 mri_convert --all-info ProgramName: mri_convert ProgramArguments: mri_convert --all-info ProgramVersion: 7.3.0 TimeStamp: 2022/07/29-17:28:43-GMT BuildTime: Jul 17 2022 18:43:07 BuildStamp: freesurfer-darwin-macOS-7.3.0-20220717-7725d89 User: mbm3668 Machine: PSYC-A30765 Platform: Darwin PlatformVersion: 21.6.0 CompilerName: Clang CompilerVersion: 12.0.0 FLIRT version 6.0 bbregister 7.3.0 mri_cvs_register 7.3.0 ProgramName: dmri_motion ProgramArguments: /Applications/freesurfer/7.3.0/bin/dmri_motion --all-info ProgramVersion: 7.3.0 TimeStamp: 2022/07/29-17:28:43-GMT BuildTime: Jul 17 2022 18:43:07 BuildStamp: freesurfer-darwin-macOS-7.3.0-20220717-7725d89 User: mbm3668 Machine: PSYC-A30765 Platform: Darwin PlatformVersion: 21.6.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: dmri_train ProgramArguments: /Applications/freesurfer/7.3.0/bin/dmri_train --all-info ProgramVersion: 7.3.0 TimeStamp: 2022/07/29-17:28:43-GMT BuildTime: Jul 17 2022 18:43:07 BuildStamp: freesurfer-darwin-macOS-7.3.0-20220717-7725d89 User: mbm3668 Machine: PSYC-A30765 Platform: Darwin PlatformVersion: 21.6.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: dmri_paths ProgramArguments: /Applications/freesurfer/7.3.0/bin/dmri_paths --all-info ProgramVersion: 7.3.0 TimeStamp: 2022/07/29-17:28:43-GMT BuildTime: Jul 17 2022 18:43:07 BuildStamp: freesurfer-darwin-macOS-7.3.0-20220717-7725d89 User: mbm3668 Machine: PSYC-A30765 Platform: Darwin PlatformVersion: 21.6.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: dmri_pathstats ProgramArguments: /Applications/freesurfer/7.3.0/bin/dmri_pathstats --all-info ProgramVersion: 7.3.0 TimeStamp: 2022/07/29-17:28:43-GMT BuildTime: Jul 17 2022 18:43:07 BuildStamp: freesurfer-darwin-macOS-7.3.0-20220717-7725d89 User: mbm3668 Machine: PSYC-A30765 Platform: Darwin PlatformVersion: 21.6.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: dmri_mergepaths ProgramArguments: /Applications/freesurfer/7.3.0/bin/dmri_mergepaths --all-info ProgramVersion: 7.3.0 TimeStamp: 2022/07/29-17:28:43-GMT BuildTime: Jul 17 2022 18:43:07 BuildStamp: freesurfer-darwin-macOS-7.3.0-20220717-7725d89 User: mbm3668 Machine: PSYC-A30765 Platform: Darwin PlatformVersion: 21.6.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: dmri_group ProgramArguments: /Applications/freesurfer/7.3.0/bin/dmri_group --all-info ProgramVersion: 7.3.0 TimeStamp: 2022/07/29-17:28:44-GMT BuildTime: Jul 17 2022 18:43:07 BuildStamp: freesurfer-darwin-macOS-7.3.0-20220717-7725d89 User: mbm3668 Machine: PSYC-A30765 Platform: Darwin PlatformVersion: 21.6.0 CompilerName: Clang CompilerVersion: 12.0.0 New invocation of trac-preproc mbm3668 PSYC-A30765 Darwin PSYC-A30765 21.6.0 Darwin Kernel Version 21.6.0: Sat Jun 18 17:07:25 PDT 2022; root:xnu-8020.140.41~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 11136 PhysMem: 37G used (13G wired), 92G unused. #------------------------------------- /Applications/freesurfer/7.3.0/bin/trac-preproc #------------------------------------- #@# Image corrections Fri Jul 29 12:28:46 CDT 2022 rm -f /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig.1.bvals /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig.1.bvecs mri_convert --bvec-voxel /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/dtiprep/sub-0003107/sub-0003107_eddy_undist.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig.1.nii.gz mri_convert --bvec-voxel /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/dtiprep/sub-0003107/sub-0003107_eddy_undist.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig.1.nii.gz reading from /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/dtiprep/sub-0003107/sub-0003107_eddy_undist.nii.gz... TR=12000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (0, 1, 0) k_ras = (-0, -0, 1) writing to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig.1.nii.gz... rm -f /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig.1.bvals.tmp /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig.1.bvecs.tmp mv -f /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig.1.bvecs.tmp /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig.1.bvecs mv -f /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig.1.bvals.tmp /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig.1.bvals orientLAS /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig.1.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig_las.1.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -5.04694 mri_convert -oni 256 -onj 256 -onk 59 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc -2.8676 -2.29242 22.4042 -rt nearest /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig.1.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig_las.1.nii.gz mri_convert -oni 256 -onj 256 -onk 59 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc -2.8676 -2.29242 22.4042 -rt nearest /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig.1.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig_las.1.nii.gz reading from /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig.1.nii.gz... TR=12000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (0, 1, 0) k_ras = (-0, -0, 1) writing to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig_las.1.nii.gz... INFO: found /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig.1.bvals, copying INFO: found /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig.1.bvecs, converting to LAS mv -f /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig_las.1.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig_las.nii.gz mv -f /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig_las.1.bvecs /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig_las.bvecs mv -f /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig_las.1.bvals /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig_las.bvals mv -f /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig_las.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi.nii.gz mv -f /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig_las.bvecs /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi.bvecs mv -f /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi_orig_las.bvals /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi.bvals rm -f /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi.full.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi.bvecs.full /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi.bvals.full mri_convert --frame 0 1 2 3 4 /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb.nii.gz mri_convert --frame 0 1 2 3 4 /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb.nii.gz reading from /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/dwi.nii.gz... TR=12000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (0, 1, 0) k_ras = (-0, -0, 1) keeping frames 0 1 2 3 4 writing to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb.nii.gz... mri_concat --i /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb.nii.gz --mean --o /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 5 Allocing output Done allocing nframes = 5 Computing mean across frames Writing to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb.nii.gz bet /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb_brain_mask.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/diff #------------------------------------- #@# DWI set selection Fri Jul 29 12:30:25 CDT 2022 ln -sf dwi.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/data.nii.gz ln -sf dwi.bvecs /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/bvecs ln -sf dwi.bvals /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/bvals #------------------------------------- #@# Intra-subject registration Fri Jul 29 12:30:25 CDT 2022 bbregister --s sub-0003107 --init-fsl --dti --6 --mov /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb.nii.gz --reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/diff2anatorig.bbr.lta tmp /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354 Log file is /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/diff2anatorig.bbr.log Fri Jul 29 12:30:25 CDT 2022 setenv SUBJECTS_DIR /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep cd /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep /Applications/freesurfer/7.3.0/bin/bbregister --s sub-0003107 --init-fsl --dti --6 --mov /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb.nii.gz --reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/diff2anatorig.bbr.lta FreeSurferEnv.csh 7.3.0 Darwin PSYC-A30765 21.6.0 Darwin Kernel Version 21.6.0: Sat Jun 18 17:07:25 PDT 2022; root:xnu-8020.140.41~1/RELEASE_X86_64 x86_64 FREESURFER_HOME /Applications/freesurfer/7.3.0 mri_convert /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii mri_convert /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii reading from /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb.nii.gz... TR=12000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (0, 1, 0) k_ras = (-0, -0, 1) writing to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii... fslregister --s sub-0003107 --mov /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii --reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/reg.init.dat --niters 1 --maxangle 90 --tmp /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov Log file is /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/reg.init.dat.fslregister.log Fri Jul 29 12:30:26 CDT 2022 --s sub-0003107 --mov /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii --reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/reg.init.dat --niters 1 --maxangle 90 --tmp /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov FreeSurferEnv.csh 7.3.0 PSYC-A30765 Darwin PSYC-A30765 21.6.0 Darwin Kernel Version 21.6.0: Sat Jun 18 17:07:25 PDT 2022; root:xnu-8020.140.41~1/RELEASE_X86_64 x86_64 nIters 1 -------------------------------------- /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep mri_convert /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/brainmask.mgz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister/refvol.fslregister.nii mri_convert /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/brainmask.mgz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister/refvol.fslregister.nii reading from /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/brainmask.mgz... TR=7.65, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister/refvol.fslregister.nii... -------------------------------------- /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep mri_convert /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister/movvol.fslregister.nii --frame 0 mri_convert /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister/movvol.fslregister.nii --frame 0 reading from /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii... TR=12000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (0, 1, 0) k_ras = (-0, -0, 1) keeping frame 0 writing to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister/movvol.fslregister.nii... Mov determinant is -5.04694 /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep tkregister2_cmdl --mov /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister/movvol.fslregister.nii --reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister/reg0.12405.dat --targ brainmask --fstarg --regheader --fslregout /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/reg.init.dat.fsl.mat0 --s sub-0003107 --noedit target volume brainmask movable volume /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister/movvol.fslregister.nii reg file /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister/reg0.12405.dat LoadVol 0 ZeroCRAS 0 7.3.0 Diagnostic Level -1 INFO: loading target /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/brainmask.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 /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.36720 0.00000 0.00000 175.00160; 0.00000 0.00000 2.70000 -79.65000; 0.00000 -1.36720 0.00000 175.00160; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.00000 0.00000 0.00000 0.41562; 0.00000 0.00000 1.00000 0.79958; 0.00000 -1.00000 0.00000 -2.66023; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 1.00000 0.00000 0.00000 0.41562; 0.00000 0.00000 1.00000 0.79958; 0.00000 -1.00000 0.00000 -2.66023; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = sub-0003107 RegMat --------------------------- 1.00000 0.00000 0.00000 0.41562; 0.00000 0.00000 1.00000 0.79958; 0.00000 -1.00000 0.00000 -2.66023; 0.00000 0.00000 0.00000 1.00000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -5.04694, ref det = -1 Fri Jul 29 12:30:27 CDT 2022 /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep flirt.fsl -ref /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister/refvol.fslregister.nii -in /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister/fslmat0.trans.mat -schedule /Applications/freesurfer/7.3.0/bin/fsl.5.0.2.xyztrans.sch -init /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/reg.init.dat.fsl.mat0 Fri Jul 29 12:30:40 CDT 2022 /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep flirt.fsl -ref /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister/refvol.fslregister.nii -in /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/reg.init.dat.fsl.mat -init /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/fslregister/fslmat0.trans.mat -schedule /Applications/freesurfer/7.3.0/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s sub-0003107 --mov /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii --targ brainmask --fstarg --reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/reg.init.dat --fslreg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/reg.init.dat.fsl.mat --noedit ---- FSL registration matrix -------- 0.99990 -0.00891 0.01061 -46.45948; 0.01070 0.00952 -0.99990 208.04492; 0.00881 0.99991 0.00961 -50.79567; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- target volume brainmask movable volume /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii reg file /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/reg.init.dat LoadVol 0 ZeroCRAS 0 7.3.0 Diagnostic Level -1 INFO: loading target /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/brainmask.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 /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii Tmov: -------------------- -1.36720 0.00000 0.00000 175.00160; 0.00000 0.00000 2.70000 -79.65000; 0.00000 -1.36720 0.00000 175.00160; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -5.04694, ref det = -1 ---- Input registration matrix (computed) -------- 0.99990 -0.00881 0.01070 -0.15964; -0.01061 0.00961 0.99990 3.95663; -0.00891 -0.99992 0.00952 -1.46280; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 0.99990 -0.00881 0.01070 -0.15964; -0.01061 0.00961 0.99990 3.95663; -0.00891 -0.99992 0.00952 -1.46280; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = sub-0003107 RegMat --------------------------- 0.99990 -0.00881 0.01070 -0.15964; -0.01061 0.00961 0.99990 3.95663; -0.00891 -0.99992 0.00952 -1.46280; 0.00000 0.00000 0.00000 1.00000; WARNING: possible left-right reversal Started at Fri Jul 29 12:30:26 CDT 2022 Ended at Fri Jul 29 12:31:06 CDT 2022 fslregister Done To check results, run: tkregisterfv --mov /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii --reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/reg.init.dat --surf orig mri_segreg --mov /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii --init-reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/reg.init.dat --out-reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/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 7.3.0 setenv SUBJECTS_DIR /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep cd /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep mri_segreg --mov /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii --init-reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/reg.init.dat --out-reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/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 PSYC-A30765 machine x86_64 user mbm3668 movvol /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii regfile /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/reg.init.dat subject sub-0003107 dof 6 outregfile /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/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 1659713994 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99990 -0.00881 0.01070 -0.15964; -0.01061 0.00961 0.99990 3.95663; -0.00891 -0.99992 0.00952 -1.46280; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/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 1.036679 1 -25.0 -25.0 25.0 1.041467 2 -25.0 25.0 -25.0 0.983165 3 -25.0 25.0 25.0 1.035026 4 25.0 -25.0 -25.0 0.989372 5 25.0 -25.0 25.0 1.011044 6 25.0 25.0 -25.0 1.000978 7 25.0 25.0 25.0 1.024684 REL: 8 0.546076 8.122415 1.015302 rel = 0.537846 Initial costs ---------------- Number of surface hits 2499 WM Intensity 2755.5487 +/- 795.0703 Ctx Intensity 3669.3031 +/- 1470.0121 Pct Contrast 23.6642 +/- 39.1864 Cost 0.5461 RelCost 0.5378 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9819 0.9819 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9315 0.9315 0.0 8 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 4.0000 0.9284 0.9284 0.0 12 -4.0000 -4.0000 -4.0000 0.0000 0.0000 -4.0000 0.9032 0.9032 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8075 0.8075 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7729 0.7729 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.7654 0.7654 0.0 256 0.0000 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.6971 0.6971 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6455 0.6455 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.4867 0.4867 0.0 Brute Force -------------------------- Min cost was 0.486732 Number of iterations 729 Search time 0.987157 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 = 0.486732 6 0.382 -4.000 0.000 0.000 0.000 0.000 0.4799659374 8 0.260 -4.000 0.000 0.000 0.000 0.000 0.4798066482 10 0.318 -4.000 0.000 0.000 0.000 0.000 0.4788196210 11 0.319 -4.000 0.000 0.000 0.000 0.000 0.4788168625 12 0.324 -4.000 0.000 0.000 0.000 0.000 0.4788117704 14 0.323 -4.000 0.000 0.000 0.000 0.000 0.4788116275 17 0.323 -3.000 0.000 0.000 0.000 0.000 0.3227962946 18 0.323 -1.382 0.000 0.000 0.000 0.000 0.3103697214 19 0.323 -2.123 0.000 0.000 0.000 0.000 0.2635569602 23 0.323 -2.091 0.000 0.000 0.000 0.000 0.2629839747 25 0.323 -2.076 0.000 0.000 0.000 0.000 0.2628137309 26 0.323 -2.072 0.000 0.000 0.000 0.000 0.2628017264 27 0.323 -2.071 0.000 0.000 0.000 0.000 0.2628016633 33 0.323 -2.071 -0.618 0.000 0.000 0.000 0.2257688484 35 0.323 -2.071 -0.770 0.000 0.000 0.000 0.2224452466 38 0.323 -2.071 -0.755 0.000 0.000 0.000 0.2222650370 40 0.323 -2.071 -0.757 0.000 0.000 0.000 0.2222610297 48 0.323 -2.071 -0.757 0.382 0.000 0.000 0.2123556007 50 0.323 -2.071 -0.757 0.520 0.000 0.000 0.2110321708 53 0.323 -2.071 -0.757 0.467 0.000 0.000 0.2096266323 56 0.323 -2.071 -0.757 0.466 0.000 0.000 0.2096254233 65 0.323 -2.071 -0.757 0.466 0.019 0.000 0.2094198728 67 0.323 -2.071 -0.757 0.466 0.022 0.000 0.2094040993 68 0.323 -2.071 -0.757 0.466 0.024 0.000 0.2093996451 76 0.323 -2.071 -0.757 0.466 0.024 0.153 0.2073929017 77 0.323 -2.071 -0.757 0.466 0.024 0.145 0.2072487805 78 0.323 -2.071 -0.757 0.466 0.024 0.108 0.2066210805 80 0.323 -2.071 -0.757 0.466 0.024 0.095 0.2065361324 82 0.323 -2.071 -0.757 0.466 0.024 0.096 0.2065347551 powell nthiter 1: fret = 0.206535 91 0.253 -2.071 -0.757 0.466 0.024 0.096 0.2055544531 92 0.241 -2.071 -0.757 0.466 0.024 0.096 0.2055394895 93 0.243 -2.071 -0.757 0.466 0.024 0.096 0.2055305157 94 0.246 -2.071 -0.757 0.466 0.024 0.096 0.2055250992 96 0.247 -2.071 -0.757 0.466 0.024 0.096 0.2055249871 106 0.247 -2.065 -0.757 0.466 0.024 0.096 0.2054789776 107 0.247 -2.060 -0.757 0.466 0.024 0.096 0.2054735787 116 0.247 -2.060 -0.973 0.466 0.024 0.096 0.2035542301 117 0.247 -2.060 -0.923 0.466 0.024 0.096 0.2010574010 118 0.247 -2.060 -0.878 0.466 0.024 0.096 0.1998006962 120 0.247 -2.060 -0.870 0.466 0.024 0.096 0.1997361333 121 0.247 -2.060 -0.867 0.466 0.024 0.096 0.1997319017 122 0.247 -2.060 -0.868 0.466 0.024 0.096 0.1997310699 133 0.247 -2.060 -0.868 0.522 0.024 0.096 0.1991591062 134 0.247 -2.060 -0.868 0.503 0.024 0.096 0.1988397815 143 0.247 -2.060 -0.868 0.503 0.088 0.096 0.1976502469 145 0.247 -2.060 -0.868 0.503 0.082 0.096 0.1976324836 147 0.247 -2.060 -0.868 0.503 0.083 0.096 0.1976322353 155 0.247 -2.060 -0.868 0.503 0.083 0.081 0.1973126859 158 0.247 -2.060 -0.868 0.503 0.083 0.065 0.1971076827 159 0.247 -2.060 -0.868 0.503 0.083 0.064 0.1971002278 161 0.247 -2.060 -0.868 0.503 0.083 0.061 0.1970944517 powell nthiter 2: fret = 0.197094 171 0.203 -2.060 -0.868 0.503 0.083 0.061 0.1969100626 172 0.213 -2.060 -0.868 0.503 0.083 0.061 0.1968102486 173 0.220 -2.060 -0.868 0.503 0.083 0.061 0.1968030215 174 0.218 -2.060 -0.868 0.503 0.083 0.061 0.1968010875 187 0.218 -2.063 -0.868 0.503 0.083 0.061 0.1967876692 198 0.218 -2.063 -0.879 0.503 0.083 0.061 0.1964707373 199 0.218 -2.063 -0.894 0.503 0.083 0.061 0.1963254293 200 0.218 -2.063 -0.893 0.503 0.083 0.061 0.1963230385 201 0.218 -2.063 -0.892 0.503 0.083 0.061 0.1963225461 213 0.218 -2.063 -0.892 0.502 0.083 0.061 0.1963111290 214 0.218 -2.063 -0.892 0.492 0.083 0.061 0.1962976849 216 0.218 -2.063 -0.892 0.496 0.083 0.061 0.1962860167 225 0.218 -2.063 -0.892 0.496 0.101 0.061 0.1958667478 227 0.218 -2.063 -0.892 0.496 0.110 0.061 0.1957908477 229 0.218 -2.063 -0.892 0.496 0.111 0.061 0.1957905984 238 0.218 -2.063 -0.892 0.496 0.111 0.063 0.1957886709 241 0.188 -2.067 -0.916 0.490 0.139 0.066 0.1956657215 powell nthiter 3: fret = 0.195789 249 0.193 -2.063 -0.892 0.496 0.111 0.063 0.1956142840 250 0.201 -2.063 -0.892 0.496 0.111 0.063 0.1955877219 251 0.199 -2.063 -0.892 0.496 0.111 0.063 0.1955848251 263 0.199 -2.064 -0.892 0.496 0.111 0.063 0.1955842216 274 0.199 -2.064 -0.893 0.496 0.111 0.063 0.1955811195 286 0.199 -2.064 -0.893 0.486 0.111 0.063 0.1955386531 287 0.199 -2.064 -0.893 0.489 0.111 0.063 0.1955287956 288 0.199 -2.064 -0.893 0.490 0.111 0.063 0.1955285628 296 0.199 -2.064 -0.893 0.490 0.115 0.063 0.1954275061 298 0.199 -2.064 -0.893 0.490 0.138 0.063 0.1953798805 299 0.199 -2.064 -0.893 0.490 0.127 0.063 0.1952714667 313 0.180 -2.065 -0.894 0.483 0.143 0.063 0.1951998989 319 0.188 -2.065 -0.894 0.485 0.137 0.063 0.1951409826 powell nthiter 4: fret = 0.195141 346 0.188 -2.077 -0.894 0.485 0.137 0.063 0.1951024081 347 0.188 -2.073 -0.894 0.485 0.137 0.063 0.1950907616 358 0.188 -2.073 -0.898 0.485 0.137 0.063 0.1950810859 359 0.188 -2.073 -0.897 0.485 0.137 0.063 0.1950792772 371 0.188 -2.073 -0.897 0.474 0.137 0.063 0.1949969954 372 0.188 -2.073 -0.897 0.475 0.137 0.063 0.1949907923 373 0.188 -2.073 -0.897 0.476 0.137 0.063 0.1949894062 381 0.188 -2.073 -0.897 0.476 0.137 0.044 0.1948767200 383 0.188 -2.073 -0.897 0.476 0.137 0.046 0.1948752140 384 0.188 -2.073 -0.897 0.476 0.137 0.047 0.1948746986 387 0.169 -2.074 -0.898 0.470 0.153 0.047 0.1948523319 391 0.176 -2.074 -0.897 0.472 0.147 0.047 0.1947933526 392 0.177 -2.074 -0.897 0.472 0.147 0.047 0.1947930267 393 0.177 -2.074 -0.897 0.472 0.147 0.047 0.1947929893 395 0.177 -2.074 -0.897 0.472 0.147 0.047 0.1947928390 powell nthiter 5: fret = 0.194793 406 0.173 -2.074 -0.897 0.472 0.147 0.047 0.1947792837 407 0.171 -2.074 -0.897 0.472 0.147 0.047 0.1947785276 418 0.171 -2.087 -0.897 0.472 0.147 0.047 0.1946802388 419 0.171 -2.085 -0.897 0.472 0.147 0.047 0.1946738492 420 0.171 -2.084 -0.897 0.472 0.147 0.047 0.1946734957 430 0.171 -2.084 -0.894 0.472 0.147 0.047 0.1946426583 433 0.171 -2.084 -0.893 0.472 0.147 0.047 0.1946397725 434 0.171 -2.084 -0.892 0.472 0.147 0.047 0.1946397298 445 0.171 -2.084 -0.892 0.463 0.147 0.047 0.1945590505 446 0.171 -2.084 -0.892 0.465 0.147 0.047 0.1945563256 456 0.171 -2.084 -0.892 0.465 0.147 0.044 0.1945518858 465 0.174 -2.084 -0.892 0.466 0.144 0.044 0.1945454579 466 0.174 -2.084 -0.892 0.466 0.144 0.044 0.1945452302 467 0.174 -2.084 -0.892 0.466 0.145 0.044 0.1945449838 469 0.173 -2.084 -0.892 0.465 0.145 0.044 0.1945448710 475 0.170 -2.094 -0.886 0.459 0.143 0.040 0.1944637219 482 0.170 -2.094 -0.886 0.459 0.143 0.040 0.1944633285 485 0.170 -2.095 -0.886 0.458 0.143 0.040 0.1944629234 powell nthiter 6: fret = 0.194463 502 0.169 -2.095 -0.886 0.458 0.143 0.040 0.1944612155 503 0.168 -2.095 -0.886 0.458 0.143 0.040 0.1944607453 512 0.172 -2.094 -0.885 0.460 0.140 0.040 0.1944502111 513 0.171 -2.094 -0.885 0.460 0.140 0.040 0.1944499098 551 0.171 -2.094 -0.885 0.460 0.140 0.041 0.1944493509 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 1.008101 1 -25.0 -25.0 25.0 1.029518 2 -25.0 25.0 -25.0 0.980847 3 -25.0 25.0 25.0 1.023942 4 25.0 -25.0 -25.0 0.979679 5 25.0 -25.0 25.0 0.987135 6 25.0 25.0 -25.0 1.052641 7 25.0 25.0 25.0 1.025592 REL: 8 0.194449 8.087456 1.010932 rel = 0.192347 Number of iterations 6 Min cost was 0.194449 Number of FunctionCalls 567 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.764093 sec Parameters at optimum (transmm) 0.17147 -2.09438 -0.88546 Parameters at optimum (rotdeg) 0.45959 0.13965 0.04102 Final costs ---------------- Number of surface hits 2499 WM Intensity 2500.1910 +/- 522.7987 Ctx Intensity 3393.6663 +/- 785.8662 Pct Contrast 29.2438 +/- 25.2861 Cost 0.1944 RelCost 0.5378 Reg at min cost was 0.99989 -0.01126 0.01002 0.00551; -0.00982 0.01762 0.99980 1.87374; -0.01143 -0.99978 0.01751 -2.31608; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/bbr.pass1.dat, type = 14 Original Reg 0.99990 -0.00881 0.01070 -0.15964; -0.01061 0.00961 0.99990 3.95663; -0.00891 -0.99992 0.00952 -1.46280; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00002 0.00245 0.00067 -0.16515; -0.00079 -0.00801 0.00010 2.08289; 0.00252 -0.00013 -0.00799 0.85328; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.409878 Computing change in rh position Surface-RMS-Diff-mm 2.419825 0.315953 3.067838 mri_segreg done mri_segreg --mov /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii --init-reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/bbr.pass1.dat --out-reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/diff2anatorig.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/diff2anatorig.bbr.dat.mincost --dof 6 --nmax 36 --param /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/diff2anatorig.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.3.0 setenv SUBJECTS_DIR /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep cd /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep mri_segreg --mov /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii --init-reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/bbr.pass1.dat --out-reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/diff2anatorig.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/diff2anatorig.bbr.dat.mincost --dof 6 --nmax 36 --param /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/diff2anatorig.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Darwin hostname PSYC-A30765 machine x86_64 user mbm3668 movvol /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/template.nii regfile /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/tmp.bbregister.12354/bbr.pass1.dat subject sub-0003107 dof 6 outregfile /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/diff2anatorig.bbr.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 1659443120 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99989 -0.01126 0.01002 0.00551; -0.00982 0.01762 0.99980 1.87374; -0.01143 -0.99978 0.01751 -2.31608; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/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 1.016394 1 -25.0 -25.0 25.0 0.997621 2 -25.0 25.0 -25.0 0.975046 3 -25.0 25.0 25.0 1.038982 4 25.0 -25.0 -25.0 0.997430 5 25.0 -25.0 25.0 1.010436 6 25.0 25.0 -25.0 1.013604 7 25.0 25.0 25.0 1.006812 REL: 8 0.206179 8.056326 1.007041 rel = 0.204738 Initial costs ---------------- Number of surface hits 251395 WM Intensity 2506.5092 +/- 550.0642 Ctx Intensity 3415.9916 +/- 795.0318 Pct Contrast 29.6781 +/- 25.9048 Cost 0.2062 RelCost 0.2047 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.2065 0.2065 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.2029 0.2029 0.0 30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.2008 0.2008 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.2000 0.2000 0.0 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.1993 0.1993 0.0 274 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.1987 0.1987 0.0 277 0.0000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1986 0.1986 0.0 278 0.0000 -0.1000 0.0000 -0.1000 0.1000 0.1000 0.1969 0.1969 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1944 0.1944 0.0 Brute Force -------------------------- Min cost was 0.194449 Number of iterations 729 Search time 0.970588 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 = 0.206179 7 -0.026 0.000 0.000 0.000 0.000 0.000 0.2060314808 8 -0.038 0.000 0.000 0.000 0.000 0.000 0.2060222938 9 -0.035 0.000 0.000 0.000 0.000 0.000 0.2060222744 11 -0.036 0.000 0.000 0.000 0.000 0.000 0.2060221766 18 -0.036 0.078 0.000 0.000 0.000 0.000 0.2053306705 20 -0.036 0.069 0.000 0.000 0.000 0.000 0.2053172859 21 -0.036 0.070 0.000 0.000 0.000 0.000 0.2053171447 29 -0.036 0.070 0.013 0.000 0.000 0.000 0.2052243575 30 -0.036 0.070 0.041 0.000 0.000 0.000 0.2051616468 31 -0.036 0.070 0.035 0.000 0.000 0.000 0.2051589316 32 -0.036 0.070 0.036 0.000 0.000 0.000 0.2051588706 40 -0.036 0.070 0.036 -0.100 0.000 0.000 0.2043647667 41 -0.036 0.070 0.036 -0.089 0.000 0.000 0.2043286453 42 -0.036 0.070 0.036 -0.081 0.000 0.000 0.2043234909 43 -0.036 0.070 0.036 -0.083 0.000 0.000 0.2043231778 51 -0.036 0.070 0.036 -0.083 0.042 0.000 0.2042581713 52 -0.036 0.070 0.036 -0.083 0.029 0.000 0.2042391114 54 -0.036 0.070 0.036 -0.083 0.030 0.000 0.2042387110 56 -0.036 0.070 0.036 -0.083 0.032 0.000 0.2042386662 64 -0.036 0.070 0.036 -0.083 0.032 0.173 0.2007974631 65 -0.036 0.070 0.036 -0.083 0.032 0.177 0.2007945673 68 -0.036 0.070 0.036 -0.083 0.032 0.178 0.2007942274 powell nthiter 1: fret = 0.200794 76 0.026 0.070 0.036 -0.083 0.032 0.178 0.2003540432 78 0.036 0.070 0.036 -0.083 0.032 0.178 0.2003474601 80 0.035 0.070 0.036 -0.083 0.032 0.178 0.2003471222 81 0.034 0.070 0.036 -0.083 0.032 0.178 0.2003470997 89 0.034 0.038 0.036 -0.083 0.032 0.178 0.2002137371 91 0.034 0.039 0.036 -0.083 0.032 0.178 0.2002136709 100 0.034 0.039 0.073 -0.083 0.032 0.178 0.2000894714 111 0.034 0.039 0.073 -0.130 0.032 0.178 0.2000243861 112 0.034 0.039 0.073 -0.113 0.032 0.178 0.1999871590 113 0.034 0.039 0.073 -0.112 0.032 0.178 0.1999865176 114 0.034 0.039 0.073 -0.109 0.032 0.178 0.1999860709 125 0.034 0.039 0.073 -0.109 0.021 0.178 0.1999724053 126 0.034 0.039 0.073 -0.109 0.020 0.178 0.1999712630 130 0.034 0.039 0.073 -0.109 0.013 0.178 0.1999682105 140 0.034 0.039 0.073 -0.109 0.013 0.199 0.1998046924 141 0.034 0.039 0.073 -0.109 0.013 0.222 0.1997786539 142 0.034 0.039 0.073 -0.109 0.013 0.214 0.1997709702 powell nthiter 2: fret = 0.199771 152 0.051 0.039 0.073 -0.109 0.013 0.214 0.1997152723 154 0.053 0.039 0.073 -0.109 0.013 0.214 0.1997149281 162 0.053 0.026 0.073 -0.109 0.013 0.214 0.1996703227 163 0.053 0.013 0.073 -0.109 0.013 0.214 0.1996662830 164 0.053 0.018 0.073 -0.109 0.013 0.214 0.1996626387 175 0.053 0.018 0.075 -0.109 0.013 0.214 0.1996612700 176 0.053 0.018 0.076 -0.109 0.013 0.214 0.1996612065 185 0.053 0.018 0.076 -0.116 0.013 0.214 0.1996524365 186 0.053 0.018 0.076 -0.117 0.013 0.214 0.1996524308 195 0.053 0.018 0.076 -0.117 0.015 0.214 0.1996515612 205 0.053 0.018 0.076 -0.117 0.015 0.235 0.1996179233 207 0.053 0.018 0.076 -0.117 0.015 0.230 0.1996139203 208 0.053 0.018 0.076 -0.117 0.015 0.229 0.1996138965 powell nthiter 3: fret = 0.199614 217 0.056 0.018 0.076 -0.117 0.015 0.229 0.1996062441 218 0.062 0.018 0.076 -0.117 0.015 0.229 0.1996034230 219 0.061 0.018 0.076 -0.117 0.015 0.229 0.1996027099 228 0.061 0.011 0.076 -0.117 0.015 0.229 0.1996017617 230 0.061 0.014 0.076 -0.117 0.015 0.229 0.1996001366 241 0.061 0.014 0.082 -0.117 0.015 0.229 0.1995935708 251 0.061 0.014 0.082 -0.122 0.015 0.229 0.1995913098 261 0.061 0.014 0.082 -0.122 0.014 0.229 0.1995911494 262 0.061 0.014 0.082 -0.122 0.013 0.229 0.1995908519 272 0.061 0.014 0.082 -0.122 0.013 0.241 0.1995896563 273 0.061 0.014 0.082 -0.122 0.013 0.235 0.1995851493 276 0.069 0.010 0.087 -0.127 0.011 0.241 0.1995743647 283 0.069 0.010 0.087 -0.127 0.011 0.241 0.1995740834 287 0.069 0.010 0.087 -0.127 0.011 0.241 0.1995740759 powell nthiter 4: fret = 0.199574 306 0.069 0.011 0.087 -0.127 0.011 0.241 0.1995736785 307 0.069 0.012 0.087 -0.127 0.011 0.241 0.1995736118 318 0.069 0.012 0.085 -0.127 0.011 0.241 0.1995735716 320 0.069 0.012 0.086 -0.127 0.011 0.241 0.1995733586 339 0.069 0.012 0.086 -0.127 0.012 0.241 0.1995731581 346 0.070 0.012 0.087 -0.127 0.012 0.242 0.1995730197 347 0.069 0.012 0.087 -0.127 0.012 0.242 0.1995730070 348 0.069 0.012 0.086 -0.127 0.012 0.242 0.1995729583 352 0.069 0.012 0.086 -0.127 0.012 0.242 0.1995729482 353 0.069 0.012 0.086 -0.127 0.012 0.242 0.1995729264 powell nthiter 5: fret = 0.199573 365 0.069 0.012 0.086 -0.127 0.012 0.240 0.1995727778 powell nthiter 6: fret = 0.199573 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 1.016687 1 -25.0 -25.0 25.0 0.996290 2 -25.0 25.0 -25.0 0.974922 3 -25.0 25.0 25.0 1.039424 4 25.0 -25.0 -25.0 0.995796 5 25.0 -25.0 25.0 1.010608 6 25.0 25.0 -25.0 1.015480 7 25.0 25.0 25.0 1.007473 REL: 8 0.199573 8.056680 1.007085 rel = 0.198169 Number of iterations 6 Min cost was 0.199573 Number of FunctionCalls 486 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 33.279081 sec Parameters at optimum (transmm) 0.06920 0.01171 0.08646 Parameters at optimum (rotdeg) -0.12688 0.01203 0.24012 Final costs ---------------- Number of surface hits 251395 WM Intensity 2503.2394 +/- 546.1842 Ctx Intensity 3414.3929 +/- 775.1797 Pct Contrast 29.8411 +/- 25.5627 Cost 0.1996 RelCost 0.2047 Reg at min cost was 0.99992 -0.01153 0.00584 0.06639; -0.00566 0.01536 0.99987 1.88032; -0.01162 -0.99982 0.01529 -2.23377; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/diff2anatorig.bbr.dat, type = 14 Original Reg 0.99989 -0.01126 0.01002 0.00551; -0.00982 0.01762 0.99980 1.87374; -0.01143 -0.99978 0.01751 -2.31608; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00003 0.00027 0.00419 -0.06088; -0.00417 0.00226 -0.00007 -0.00658; 0.00019 0.00003 0.00222 -0.08231; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.184013 Computing change in rh position Surface-RMS-Diff-mm 0.213070 0.083774 0.444444 mri_segreg done MinCost: 0.199573 2503.239439 3414.392853 29.841098 tkregister2_cmdl --mov /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb.nii.gz --reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/diff2anatorig.bbr.dat --noedit --ltaout /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/diff2anatorig.bbr.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb.nii.gz reg file /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/diff2anatorig.bbr.dat LoadVol 0 ZeroCRAS 0 7.3.0 Diagnostic Level -1 ---- Input registration matrix -------- 0.99992 -0.01153 0.00584 0.06639; -0.00566 0.01536 0.99987 1.88032; -0.01162 -0.99982 0.01529 -2.23377; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/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 /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb.nii.gz Tmov: -------------------- -1.36720 0.00000 0.00000 175.00160; 0.00000 0.00000 2.70000 -79.65000; 0.00000 -1.36720 0.00000 175.00160; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99992 -0.01153 0.00584 0.06639; -0.00566 0.01536 0.99987 1.88032; -0.01162 -0.99982 0.01529 -2.23377; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = sub-0003107 RegMat --------------------------- 0.99992 -0.01153 0.00584 0.06639; -0.00566 0.01536 0.99987 1.88032; -0.01162 -0.99982 0.01529 -2.23377; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Fri Jul 29 12:30:25 CDT 2022 Ended at Fri Jul 29 12:31:53 CDT 2022 BBR-Run-Time-Sec 88 bbregister Done To check results, run: tkregisterfv --mov /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/lowb.nii.gz --reg /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/diff2anatorig.bbr.lta --surfs --sd /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep lta_convert --inlta /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/diff2anatorig.bbr.lta --invert --outlta /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta 7.3.0 --inlta: /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/diff2anatorig.bbr.lta input LTA transform. --invert: will invert transform. --outlta: /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta output LTA. LTA read, type : 1 0.99992 0.01162 -0.00566 0.48711; -0.01153 0.99982 0.01536 0.02112; 0.00584 -0.01529 0.99987 -1.06201; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta... lta_convert successful. mri_convert /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/aparc+aseg.mgz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/aparc+aseg.mgz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg.nii.gz reading from /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/aparc+aseg.mgz... TR=7.65, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg.nii.gz... mri_binarize --i /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg.nii.gz --min .5 --dilate 4 --erode 2 --o /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg_mask.nii.gz 7.3.0 cwd /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep cmdline mri_binarize --i /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg.nii.gz --min .5 --dilate 4 --erode 2 --o /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg_mask.nii.gz sysname Darwin hostname PSYC-A30765 machine x86_64 user mbm3668 input /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg.nii.gz frame 0 nErode3d 2 nErode2d 0 output /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg_mask.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 1169534 values in range Dilating 4 voxels in 3d Eroding 2 voxels in 3d Counting number of voxels in first frame Found 1609388 voxels in final mask Writing output to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg_mask.nii.gz Count: 1609388 1609388.000000 16777216 9.592700 mri_binarize done mri_binarize --i /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/aparc+aseg.mgz --match 2 41 7 46 172 177 77 --o /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/White-Matter.nii.gz 7.3.0 cwd /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep cmdline mri_binarize --i /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/aparc+aseg.mgz --match 2 41 7 46 172 177 77 --o /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/White-Matter.nii.gz sysname Darwin hostname PSYC-A30765 machine x86_64 user mbm3668 input /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/White-Matter.nii.gz Binarizing based on matching values nMatch 7 0 2 1 41 2 7 3 46 4 172 5 177 6 77 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 507378 values in range Counting number of voxels in first frame Found 507377 voxels in final mask Writing output to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/White-Matter.nii.gz Count: 507377 507377.000000 16777216 3.024203 mri_binarize done mri_binarize --i /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/aparc+aseg.mgz --match 2 41 7 46 172 177 77 28 60 16 173 174 175 --o /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/White-Matter++.nii.gz 7.3.0 cwd /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep cmdline mri_binarize --i /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/aparc+aseg.mgz --match 2 41 7 46 172 177 77 28 60 16 173 174 175 --o /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/White-Matter++.nii.gz sysname Darwin hostname PSYC-A30765 machine x86_64 user mbm3668 input /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep/sub-0003107/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 13 0 2 1 41 2 7 3 46 4 172 5 177 6 77 7 28 8 60 9 16 10 173 11 174 12 175 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 537583 values in range Counting number of voxels in first frame Found 537582 voxels in final mask Writing output to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/White-Matter++.nii.gz Count: 537582 537582.000000 16777216 3.204238 mri_binarize done mri_convert -at /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/diff/aparc+aseg.bbr.nii.gz mri_convert -at /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/diff/aparc+aseg.bbr.nii.gz reading from /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg.nii.gz... TR=7.65, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Reading transformation from file /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99992 -0.01153 0.00584 -0.48062; 0.01162 0.99982 -0.01529 -0.04302; -0.00566 0.01536 0.99987 1.06430; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/diff/aparc+aseg.bbr.nii.gz... mri_convert -at /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg_mask.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/diff/aparc+aseg_mask.bbr.nii.gz mri_convert -at /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg_mask.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/diff/aparc+aseg_mask.bbr.nii.gz reading from /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg_mask.nii.gz... TR=7.65, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Reading transformation from file /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99992 -0.01153 0.00584 -0.48062; 0.01162 0.99982 -0.01529 -0.04302; -0.00566 0.01536 0.99987 1.06430; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/diff/aparc+aseg_mask.bbr.nii.gz... mri_convert -at /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/White-Matter.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/diff/White-Matter.bbr.nii.gz mri_convert -at /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/White-Matter.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/diff/White-Matter.bbr.nii.gz reading from /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/White-Matter.nii.gz... TR=7.65, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Reading transformation from file /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99992 -0.01153 0.00584 -0.48062; 0.01162 0.99982 -0.01529 -0.04302; -0.00566 0.01536 0.99987 1.06430; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/diff/White-Matter.bbr.nii.gz... mri_convert -at /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/White-Matter++.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/diff/White-Matter++.bbr.nii.gz mri_convert -at /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/White-Matter++.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/diff/White-Matter++.bbr.nii.gz reading from /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/White-Matter++.nii.gz... TR=7.65, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Reading transformation from file /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99992 -0.01153 0.00584 -0.48062; 0.01162 0.99982 -0.01529 -0.04302; -0.00566 0.01536 0.99987 1.06430; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/diff/White-Matter++.bbr.nii.gz... mri_convert -at /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz mri_convert -at /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz reading from /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz... error: niiRead(): error opening file /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/sub-0003107/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz Darwin PSYC-A30765 21.6.0 Darwin Kernel Version 21.6.0: Sat Jun 18 17:07:25 PDT 2022; root:xnu-8020.140.41~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Jul 29 12:32:15 CDT 2022