Freesurfer September 2021

freesurfer@nmr.mgh.harvard.edu

76 participants
107 discussions

Longitudinal Hypothalamic Subunits
by Pedersen, Walker Scott 29 Sep '21

29 Sep '21

I see that generating the hippocampal subfields in the longitudinal pipeline has its own script (segmentHA_T1_long.sh), but am not seeing a corresponding script or command to do the same for the hypothalamic subunits. Would simply running mri_segment_hypothalamic_subunits on my subject_session.long.template folders get me there, or would that be violating the logic of the logitudinal pipeline, by not taking advantage of the unbiased template?

2 1

Freesurfer: Version of development version?
by Tobias Ruzok 29 Sep '21

29 Sep '21

External Email - Use Caution Dear Sir or Madam, first of all, thanks a lot for providing such a great tool like Freesurfer! I only have a minor question regarding the version I used: As I am writing a Paper for a Journal right now, I also wanted to quote the Freesurfer Version I used. We downloaded the development version of Freesurfer on 02.02.2021. But now I wanted to know if this downloaded development version is Freesurfer version 7.0 or 7.1.0/7.1.1 or even another version. Is it possible to detect the version with the information I provided? That would be really great! Thanks a lot! All the best, Tobias Ruzok

2 2

TRACULA Locating Bvecs Error
by Jacoby, John 29 Sep '21

29 Sep '21

Hi all, I'm running the trac-all -prep step and it's running into an error when looking for the bvecs: awk: fatal: cannot open file `/autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.bvecs' for reading (No such file or directory) The error is correct that dwi_orig_las.bvecs does not exist. There is however a dwi_orig_las.1.bvecs and a dwi_orig_las.2.bvecs in that same directory. Any help with this would be greatly appreciated, thank you! Best, John Command: trac-all -prep -c tracula_test_config.txt Config File: setenv SUBJECTS_DIR /autofs/cluster/bang/TAW_New/recons/default set dtroot = /autofs/cluster/bang/TAW_New/tracula set dcmroot = /autofs/cluster/bang/TAW_New/data set epifactor = 128 set echospacing = 0.69 set dob0 = 2 set interreg = 4 set subjlist = ( 180515_4PR00065 180515_4PR00065 ) set dcmlist = ( 180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512252089486946407 180515_4PR00065/DICOMs/031_dMRI_dir98_PA/MR.1.3.12.2.1107.5.2.43.67026.2018051512284637673973138 ) set pedir = ( AP PA ) Complete Log: Tue Sep 28 19:16:39 EDT 2021 /autofs/cluster/bang/TAW_New /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/trac-all -prep -jobs trac_commands.txt -c scripts/resources/tracula_test_config.txt Subject 180515_4PR00065 SUBJECTS_DIR /autofs/cluster/bang/TAW_New/recons/default FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/7.2.0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/7.2.0 build-stamp.txt: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b jj1006 launchpad.nmr.mgh.harvard.edu Linux launchpad.nmr.mgh.harvard.edu 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 131070 memorylocked unlimited maxproc 127905 maxlocks unlimited maxsignal 127905 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 32778768 2017008 27346208 124188 3415552 30235716 Swap: 67108856 686920 66421936 ######################################## Program versions: trac-all 7.2.0 mri_convert --all-info ProgramName: mri_convert ProgramArguments: mri_convert --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/09/28-23:16:39-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 FLIRT version 6.0 bbregister 7.2.0 mri_cvs_register 7.2.0 ProgramName: dmri_motion ProgramArguments: /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/dmri_motion --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/09/28-23:16:40-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_train ProgramArguments: /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/dmri_train --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/09/28-23:16:40-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_paths ProgramArguments: /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/dmri_paths --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/09/28-23:16:40-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_pathstats ProgramArguments: /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/dmri_pathstats --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/09/28-23:16:40-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_mergepaths ProgramArguments: /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/dmri_mergepaths --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/09/28-23:16:40-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: dmri_group ProgramArguments: /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/dmri_group --all-info ProgramVersion: 7.2.0 TimeStamp: 2021/09/28-23:16:40-GMT BuildTime: Jul 20 2021 18:45:50 BuildStamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b User: jj1006 Machine: launchpad.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1160.25.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 New invocation of trac-preproc jj1006 compute-0-15.nmr.mgh.harvard.edu Linux compute-0-15.nmr.mgh.harvard.edu 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 29360128 kbytes descriptors 32768 memorylocked unlimited maxproc 127909 maxlocks unlimited maxsignal 127909 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 32778856 1144720 26449592 101436 5184544 31108544 Swap: 67108860 538196 66570664 #------------------------------------- /autofs/cluster/freesurfer/centos7_x86_64/7.2.0/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Sep 28 19:16:47 EDT 2021 rm -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvals /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvecs mri_convert --bvec-voxel /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512252089486946407 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.nii.gz mri_convert --bvec-voxel /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512252089486946407 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.nii.gz reading from /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512252089486946407... Getting Series No INFO: Found 101 files in /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP INFO: Scanning for Series Number 28 Scanning Directory INFO: found 99 files in series INFO: loading series header info. RunNo = 27 WARNING: Run 1 appears to be truncated Files Found: 99, Files Expected (lRep+1): 1 FileName /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512220971428016067 Identification NumarisVer syngo MR E11 ScannerModel Prisma_fit PatientName 180515_4PR00065 Date and time StudyDate 20180515 StudyTime 114840.347000 SeriesTime 122239.413000 AcqTime 122131.110000 Acquisition parameters PulseSeq ep_b5#1 Protocol dMRI_dir98_AP PhEncDir COL EchoNo 1 FlipAngle 78 EchoTime 89.2 InversionTime -1 RepetitionTime 3230 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 27 SeriesNo 28 ImageNo 1 NImageRows 1400 NImageCols 1400 NFrames 99 SliceArraylSize 92 IsMosaic 1 ImgPos 1002.7822 1063.1628 325.3363 VolRes 1.5000 1.5000 1.5000 VolDim 140 140 92 Vc -0.9990 -0.0444 -0.0029 Vr 0.0426 -0.9342 -0.3543 Vs 0.0130 -0.3541 0.9351 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (140 140 92), nframes = 99, ismosaic=1 sdfi->UseSliceScaleFactor 0 INFO: rescale not needed datatype = 4, short=4, float=3 Could not parse NUMARIS version string syngo MR E11 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 3230, TR = 3230 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; FileName /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512220971428016067 Identification NumarisVer syngo MR E11 ScannerModel Prisma_fit PatientName 180515_4PR00065 Date and time StudyDate 20180515 StudyTime 114840.347000 SeriesTime 122239.413000 AcqTime 122131.110000 Acquisition parameters PulseSeq ep_b5#1 Protocol dMRI_dir98_AP PhEncDir COL EchoNo 1 FlipAngle 78 EchoTime 89.2 InversionTime -1 RepetitionTime 3230 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 27 SeriesNo 28 ImageNo 1 NImageRows 1400 NImageCols 1400 NFrames 99 SliceArraylSize 92 IsMosaic 1 ImgPos 98.9473 138.4093 -12.2484 VolRes 1.5000 1.5000 1.5000 VolDim 140 140 92 Vc -0.9990 -0.0444 -0.0029 Vr 0.0426 -0.9342 -0.3543 Vs 0.0130 -0.3541 0.9351 VolCenter -0.5800 11.2260 14.7653 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 1 sagrev = 0, correv =0, trarev = 0 Vs = 0.0130269 -0.3541 0.935117 INFO: no Siemens slice order reversal detected (good!). TR=3230.00, TE=89.20, TI=-1.00, flip angle=78.00 i_ras = (-0.999009, -0.0444233, -0.00290475) j_ras = (0.0425695, -0.934152, -0.354328) k_ras = (0.0130269, -0.3541, 0.935117) writing to /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.nii.gz... Saving bvals and bvecs mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.voxel_space.bvecs /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvecs mri_probedicom --i /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512252089486946407 >> /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dcminfo.dat rm -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvals /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvecs mri_convert --bvec-voxel /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/031_dMRI_dir98_PA/MR.1.3.12.2.1107.5.2.43.67026.2018051512284637673973138 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.nii.gz mri_convert --bvec-voxel /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/031_dMRI_dir98_PA/MR.1.3.12.2.1107.5.2.43.67026.2018051512284637673973138 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.nii.gz reading from /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/031_dMRI_dir98_PA/MR.1.3.12.2.1107.5.2.43.67026.2018051512284637673973138... Getting Series No INFO: Found 101 files in /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/031_dMRI_dir98_PA INFO: Scanning for Series Number 31 Scanning Directory INFO: found 99 files in series INFO: loading series header info. RunNo = 30 WARNING: Run 1 appears to be truncated Files Found: 99, Files Expected (lRep+1): 1 FileName /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/031_dMRI_dir98_PA/MR.1.3.12.2.1107.5.2.43.67026.2018051512275166034962234 Identification NumarisVer syngo MR E11 ScannerModel Prisma_fit PatientName 180515_4PR00065 Date and time StudyDate 20180515 StudyTime 114840.347000 SeriesTime 122828.358000 AcqTime 122712.317500 Acquisition parameters PulseSeq ep_b5#1 Protocol dMRI_dir98_PA PhEncDir COL EchoNo 1 FlipAngle 78 EchoTime 89.2 InversionTime -1 RepetitionTime 3230 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 1400 NImageCols 1400 NFrames 99 SliceArraylSize 92 IsMosaic 1 ImgPos 1002.7822 1063.1628 325.3363 VolRes 1.5000 1.5000 1.5000 VolDim 140 140 92 Vc -0.9990 -0.0444 -0.0029 Vr 0.0426 -0.9342 -0.3543 Vs 0.0130 -0.3541 0.9351 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (140 140 92), nframes = 99, ismosaic=1 sdfi->UseSliceScaleFactor 0 INFO: rescale not needed datatype = 3, short=4, float=3 Could not parse NUMARIS version string syngo MR E11 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 3230, TR = 3230 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; FileName /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/031_dMRI_dir98_PA/MR.1.3.12.2.1107.5.2.43.67026.2018051512275166034962234 Identification NumarisVer syngo MR E11 ScannerModel Prisma_fit PatientName 180515_4PR00065 Date and time StudyDate 20180515 StudyTime 114840.347000 SeriesTime 122828.358000 AcqTime 122712.317500 Acquisition parameters PulseSeq ep_b5#1 Protocol dMRI_dir98_PA PhEncDir COL EchoNo 1 FlipAngle 78 EchoTime 89.2 InversionTime -1 RepetitionTime 3230 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 30 SeriesNo 31 ImageNo 1 NImageRows 1400 NImageCols 1400 NFrames 99 SliceArraylSize 92 IsMosaic 1 ImgPos 98.9473 138.4093 -12.2484 VolRes 1.5000 1.5000 1.5000 VolDim 140 140 92 Vc -0.9990 -0.0444 -0.0029 Vr 0.0426 -0.9342 -0.3543 Vs 0.0130 -0.3541 0.9351 VolCenter -0.5800 11.2260 14.7653 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 1 sagrev = 0, correv =0, trarev = 0 Vs = 0.0130269 -0.3541 0.935117 INFO: no Siemens slice order reversal detected (good!). TR=3230.00, TE=89.20, TI=-1.00, flip angle=78.00 i_ras = (-0.999009, -0.0444233, -0.00290475) j_ras = (0.0425695, -0.934152, -0.354328) k_ras = (0.0130269, -0.3541, 0.935117) writing to /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.nii.gz... Saving bvals and bvecs mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.voxel_space.bvecs /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvecs mri_probedicom --i /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/031_dMRI_dir98_PA/MR.1.3.12.2.1107.5.2.43.67026.2018051512284637673973138 >> /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dcminfo.dat rm -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvals.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvecs.tmp mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvecs.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvecs mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvals.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvals orientLAS /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.1.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 3.375 mri_convert -oni 140 -onj 140 -onk 92 -oid -0.999009 -0.0444233 -0.00290475 -ojd -0.0425695 0.934152 0.354328 -okd 0.0130269 -0.3541 0.935117 -oc -0.643818 12.6272 15.2968 -rt nearest /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.1.nii.gz mri_convert -oni 140 -onj 140 -onk 92 -oid -0.999009 -0.0444233 -0.00290475 -ojd -0.0425695 0.934152 0.354328 -okd 0.0130269 -0.3541 0.935117 -oc -0.643818 12.6272 15.2968 -rt nearest /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.1.nii.gz normalizing out_i_direction: (-0.999009, -0.0444233, -0.00290475) -> (-0.999009, -0.0444233, -0.00290475) normalizing out_j_direction: (-0.0425695, 0.934152, 0.354328) -> (-0.0425695, 0.934152, 0.354328) normalizing out_k_direction: (0.0130269, -0.3541, 0.935117) -> (0.0130269, -0.3541, 0.935117) reading from /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.nii.gz... TR=3230.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999009, -0.0444233, -0.00290475) j_ras = (0.0425695, -0.934152, -0.354328) k_ras = (0.0130269, -0.3541, 0.935117) Reslicing using nearest writing to /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.1.nii.gz... INFO: found /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvals, copying INFO: found /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.1.bvecs, converting to LAS rm -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvals.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvecs.tmp mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvecs.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvecs mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvals.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvals orientLAS /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.2.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 3.375 mri_convert -oni 140 -onj 140 -onk 92 -oid -0.999009 -0.0444233 -0.00290475 -ojd -0.0425695 0.934152 0.354328 -okd 0.0130269 -0.3541 0.935117 -oc -0.643818 12.6272 15.2968 -rt nearest /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.2.nii.gz mri_convert -oni 140 -onj 140 -onk 92 -oid -0.999009 -0.0444233 -0.00290475 -ojd -0.0425695 0.934152 0.354328 -okd 0.0130269 -0.3541 0.935117 -oc -0.643818 12.6272 15.2968 -rt nearest /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.2.nii.gz normalizing out_i_direction: (-0.999009, -0.0444233, -0.00290475) -> (-0.999009, -0.0444233, -0.00290475) normalizing out_j_direction: (-0.0425695, 0.934152, 0.354328) -> (-0.0425695, 0.934152, 0.354328) normalizing out_k_direction: (0.0130269, -0.3541, 0.935117) -> (0.0130269, -0.3541, 0.935117) reading from /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.nii.gz... TR=3230.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999009, -0.0444233, -0.00290475) j_ras = (0.0425695, -0.934152, -0.354328) k_ras = (0.0130269, -0.3541, 0.935117) Reslicing using nearest writing to /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.2.nii.gz... INFO: found /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvals, copying INFO: found /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.2.bvecs, converting to LAS mri_convert --frame 0 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.1.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.1.nii.gz mri_convert --frame 0 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.1.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.1.nii.gz reading from /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.1.nii.gz... TR=3230.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999009, -0.0444233, -0.00290475) j_ras = (-0.0425695, 0.934152, 0.354328) k_ras = (0.0130269, -0.3541, 0.935117) keeping frame 0 writing to /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.1.nii.gz... mri_convert --frame 0 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.2.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.2.nii.gz mri_convert --frame 0 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.2.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.2.nii.gz reading from /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.2.nii.gz... TR=3230.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999009, -0.0444233, -0.00290475) j_ras = (-0.0425695, 0.934152, 0.354328) k_ras = (0.0130269, -0.3541, 0.935117) keeping frame 0 writing to /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.2.nii.gz... mri_concat --i /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.1.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.2.nii.gz --o /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.nii.gz ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.nii.gz cp -p /usr/pubsw/packages/fsl/6.0.4//src/topup/flirtsch/b02b0.cnf /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri topup --imain=/autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_orig_las.nii.gz --datain=/autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/acqp.txt --config=/autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/b02b0.cnf --out=/autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/topup --iout=/autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_topup.nii.gz Linux compute-0-15.nmr.mgh.harvard.edu 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Sep 28 19:53:19 EDT 2021 xfmrot /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi.eddy_parameters /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.bvecs /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi.bvecs awk: fatal: cannot open file `/autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.bvecs' for reading (No such file or directory) awk: fatal: cannot open file `/autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.bvecs' for reading (No such file or directory) ERROR: Gradient file needs to have 3 rows or 3 columns of coordinates Linux erso.nmr.mgh.harvard.edu 4.18.0-310.el8.x86_64 #1 SMP Tue Jun 8 00:24:50 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Sep 28 19:55:38 EDT 2021

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Re: [Freesurfer] recon-all mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied error
by fsbuild 27 Sep '21

27 Sep '21

External Email - Use Caution OK - fill out the form on this page and download the license.txt file, https://secure-web.cisco.com/1x188geQEK3Rrhy9C_TF54vhIgmM9qi1beEnk0Zgdzy4QT… You can copy license.txt to your home directory, e.g., if it’s in your Downloads folder from downloading via the browser, $ cp $HOME/Downloads/license.txt  $HOME/. Then you can set the environment variable FS_LICENSE to it’s location, $ export FS_LICENSE=$HOME/license.txt … check it is readable … $ cat $FS_LICENSE You can put the license.txt anywhere just as long as FS_LICENSE is set to point to it. Then try your commands again. - R.. On Sep 26, 2021, at 14:10, Banik, Rana <rana.banik(a)vanderbilt.edu> wrote:        External Email - Use Caution                External Email - Use Caution        I installed freesurfer here: banikr2@banikr:~$ which freesurfer /usr/local/freesurfer/bin/freesurferI am getting the following error while running recon-all:banikr2@banikr:~$ export SUBJECT_DIR=/home/banikr2/273_p banikr2@banikr:~$ recon-all -s sub273 -i 273_p/273_MR.nii mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/sub273/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/sub273/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551I found this from previous troubleshoot emails of freesurfer here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/10nZ_VGLWCVDFmlydatYBlFkdXTaJEnvkpD2O… I performed accordingly. Any suggestions?Rana Banik_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1OG3BAo0lmU7cE8cn9LvmHGOEYJzbtbgtwdIvUeIwpOy9kXhVQ-h2j_LveMzWwYTkZ2AqEE8r0GJeWpLjEPOHdUK_hrAe6A9nF9duhTCbe1ACFFJzElxg8IrW7vAtVlSF1RXP7Dr0UUnskPRn4eZT5x9kfwr2t9JxN_OGawnuSTnvIK_SWF89JiymqD7T0csS5MzLGkbeUHy_l-JCJTAYaDIaRkN2AG8adtZhWjjaeeAKbBu14kofu7r8rX6JautSUQCIP5jw9zJhJVfqIlHAOQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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WM or Pial edits to correct surfaces
by Alexopoulos, Dimitrios 27 Sep '21

27 Sep '21

External Email - Use Caution Hi users, We're having some issues with running some of our 2-3yo data (0.8mm isotropic) through FS7 with and without the -hires flag. There are persistent issues with the frontal lobe regions where the pial has not extended to outer surface as illustrated below. The WM surface contour look reasonable but the pial has underestimated the outer cortex resulting in an incorrect surface (below). I don't think control points will work (low intensity values in the 50-60s), and no WM to add to the WM.mgz. Any suggestion on how to push the pial surface out to capture the cortical surface?? Thx. Jim [cid:image004.png@01D752FB.04011E10] [cid:image005.jpg@01D752FB.04011E10] [cid:image001.png@01D752F8.E6507AC0] [cid:image002.png@01D752F8.E6507AC0] [cid:image006.png@01D752FB.04011E10][cid:image007.jpg@01D752FB.04011E10] ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Different volume measurements Freesurfer V7.1.1
by özenç taşkın 27 Sep '21

27 Sep '21

2 3

Re: [Freesurfer] Converting MNI to RAS on fsaverage
by Douglas N. Greve 27 Sep '21

27 Sep '21

No, the RAS in fsaverage is in MNI305 space, so no need to do the conversion. On 9/27/2021 11:22 AM, Kennedy, Bryan wrote: > Good morning, > > We are trying to conduct a meta-analysis by mapping reported MNI > dimensions (by others) on fsaverage. I know that I have to use the > following conversion: > > MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' > > in which, > > Norig = [-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] > Torig = [-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] > > When I checked TalXFM, it was just the identity maxtrix (in > fsaverage/mri/transforms/talairach.xfm). So, > > RAS = inv(Norig)*Torig*MNI; > > But based on that, MNI and RAS would be the same coordinates. For > instance: > > MNI(16 -67 39) -> RAS(16 -67 39) > > Are we missing something? Do these numbers make sense to you? > > Thanks in advance, > Bryan > >

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Re: [Freesurfer] recon-all mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied error
by fsbuild 26 Sep '21

26 Sep '21

External Email - Use Caution Hello Rana, Looks like you are missing a capital S at the end of SUBJECT or it’s SUBJECTS_DIR instead of SUBJECT_DIR. $ export SUBJECTS_DIR=/home/banikr2/273_p So the default SUBJECTS_DIR, /usr/local/freesurfer/subjects, ended up getting used, and you do not have permission to write there. - R. On Sep 26, 2021, at 14:10, Banik, Rana <rana.banik(a)vanderbilt.edu> wrote:        External Email - Use Caution                External Email - Use Caution        I installed freesurfer here: banikr2@banikr:~$ which freesurfer /usr/local/freesurfer/bin/freesurferI am getting the following error while running recon-all:banikr2@banikr:~$ export SUBJECT_DIR=/home/banikr2/273_p banikr2@banikr:~$ recon-all -s sub273 -i 273_p/273_MR.nii mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/sub273/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/sub273/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551I found this from previous troubleshoot emails of freesurfer here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/1gXITlegvJK1p_-l14FbolcoT9opnCLyCP3dD… I performed accordingly. Any suggestions?Rana Banik_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1OG3BAo0lmU7cE8cn9LvmHGOEYJzbtbgtwdIvUeIwpOy9kXhVQ-h2j_LveMzWwYTkZ2AqEE8r0GJeWpLjEPOHdUK_hrAe6A9nF9duhTCbe1ACFFJzElxg8IrW7vAtVlSF1RXP7Dr0UUnskPRn4eZT5x9kfwr2t9JxN_OGawnuSTnvIK_SWF89JiymqD7T0csS5MzLGkbeUHy_l-JCJTAYaDIaRkN2AG8adtZhWjjaeeAKbBu14kofu7r8rX6JautSUQCIP5jw9zJhJVfqIlHAOQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

2 1

recon-all mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied error
by Banik, Rana 26 Sep '21

26 Sep '21

External Email - Use Caution I installed freesurfer here: banikr2@banikr:~$ which freesurfer /usr/local/freesurfer/bin/freesurfer I am getting the following error while running recon-all: banikr2@banikr:~$ export SUBJECT_DIR=/home/banikr2/273_p banikr2@banikr:~$ recon-all -s sub273 -i 273_p/273_MR.nii mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/sub273/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/sub273/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 I found this from previous troubleshoot emails of freesurfer here: https://secure-web.cisco.com/1bocVcL-uht7sTBBGDhGvGZzup63MHVzmcTNCz1auLpZYP… which I performed accordingly. Any suggestions? Rana Banik

1 0

Freesurfer V7.1.1: recon-all meet the problem: set: No match
by 胡浩宇 26 Sep '21

26 Sep '21

External Email - Use Caution Dear Freesurfer experts, I'm a novice in using Freesurfer and I'm trying to run recon-all command to try if I can use Freesurfer to deal with the MRI data. Here is my codes: "export SUBJECTS_DIR=hcp/data/100206 mkdir -p subject1 recon-all -s sub_try -i T1w/*.nii -sd project/subject1/ -all" The codes are in quotes, in which 100206 stands for a folder containing T1w folder that have a .nii file, and project stands for the folder I want to store my result. But when I tried to run this script, I got the feedback "set: No match" and I don't know why. Could you please give me some suggestions to solve this problem? Thank you very much! Best regards, Blue

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Freesurfer September 2021