Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Re: [Freesurfer] FreeSurfer 7.1.0 VirtualBox Installation password
by fsbuild 01 Oct '21

01 Oct '21

External Email - Use Caution Sending the info to your private email shortly. - R. On Oct 1, 2021, at 14:51, Lester Melie-Garcia <lester_melie(a)yahoo.com> wrote:        External Email - Use Caution        Dear Freesurfer team,Could you provide me the password for the user 'developer' of the VM Freesurfer installation?Many thanks in advance,Best regards,Lester Melie-Garcia, PhDDepartment of Biomedical EngineeringUniversity of Basel. Switzerland._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FreeSurfer 7.1.0 VirtualBox Installation password
by Lester Melie-Garcia 01 Oct '21

01 Oct '21

External Email - Use Caution Dear Freesurfer team, Could you provide me the password for the user 'developer' of the VM Freesurfer installation? Many thanks in advance, Best regards, Lester Melie-Garcia, PhD

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Control for eTIV on Voxelwise Wholebrain Analysis?
by Wakim, Kathryn-Mary 01 Oct '21

01 Oct '21

External Email - Use Caution Hi all, I'm currently running a voxelwise whole-brain analysis on my recon-all data using the procedure outlined here: https://secure-web.cisco.com/1ltFRrUt9VeFo_xsJaFu_MKrnVu0LBNxjHernMBBefXqT5… If I am performing this analysis on volume (not cortical thickness), do I need to include eTIV as a covariate in my FSGD file? Thanks! Kamy

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What does Freesurfer do with a T2 if you do not use the t2pial flag
by Aaron Tanenbaum 01 Oct '21

01 Oct '21

External Email - Use Caution What does Freesurfer do with a T2 if you do not use the t2pial flag?

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Color LUT after coregister and reslice aparc/aseg.nii
by Ryan Wales 01 Oct '21

01 Oct '21

External Email - Use Caution Hello, I'm using fmriprep's aparcaseg_dseg.nii (still FreeSurfer code, right?) to create ROI masks. I wish to coregister and reslice this segmentation file to match the native space for another image (PET), then extract SUVR values for each ROI. However, after coregistration, the lookup values are no longer faithful to their original values. Would there be a way to view or create a new color LUT that reflects that aparcaseg_dseg.nii map in a different space? Thank you, Ryan -- Ryan Wales (he/him), M.A. Ph.D. Candidate Integrative Neuroscience Psychology Department Stony Brook University E-mail: ryan.wales(a)stonybrook.edu <ryanwales(a)stonybrook.edu>

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unpacking Diffusion data
by Nasiriavanaki, Zahra,M.D. 30 Sep '21

30 Sep '21

Hello Freesurfers, I have 6 runs of DTI data per subject in a sample of 50, and I want to unpack the dicoms, so it outputs the bval bvec values, to use in dt_recon. I realized I can use either dcm2nii or mri_convert to do this. Could you please let me know what the command should be? and also should I do it separately for each run? subject’s scan info is attached. I used the below command in dev environment but didn’t get any bval bvec values. mri_convert /${subj}/IMAGES/IM01113 /${subj}/DTI/IM_13.nii Appreciate your help. Mona 1 Localizer ok 512 512 13 1 IM00269 2 SagT2FLAIRSPACE ok 512 512 176 1 IM00273 3 SagT2FLAIRSPACE ok 512 512 171 1 IM02084 4 SagT1MPRAGE1mmiso_P3 ok 256 256 176 1 IM00449 5 SagT2FLAIRSPACE ok 512 512 227 1 IM02311 6 SagT1MPRAGE1mmiso_P3 ok 256 256 171 1 IM02482 7 SagT1MPRAGE1mmiso_P3 ok 256 256 239 1 IM02721 8 AxWaveSWI ok 288 252 88 1 IM00793 9 AxWaveSWI ok 288 252 88 1 IM00881 10 AxWaveSWI ok 288 252 81 1 IM00705 11 AxWaveSWI ok 288 252 88 1 IM00969 12 Diffusion ok 990 990 1 70 IM00970 13 Diffusion ok 110 110 74 1 IM01113 14 Diffusion ok 110 110 74 1 IM01187 15 Diffusion ok 110 110 74 1 IM01261 16 Diffusion ok 110 110 74 1 IM01335 17 Diffusion ok 110 110 1 74 IM01336 Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

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Fill between two surfaces
by I. Kelleher-Unger 30 Sep '21

30 Sep '21

External Email - Use Caution Hi there, Apologies if this is a basic question: I have two surfaces and I would like to make a ribbon/mask of the area between the surfaces. How could I go about this? Is mris_fill the right tool to use? Thanks for your help! Isaac

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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

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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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