FSL for HCP pipelines

[Yonatan Abrham]

Greetings,

Does the HCP pipeline use a different kind of FSL? I'm using the Qunex container and the way topup is used in TopupPreprocessingAll.sh is different than the usage outlined by the version of FSL I have.

Thank you,

Yonatan 

[Glasser, Matt]

No, do you have a specific question about the topup usage in the HCP Pipelines?

Matt.

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[Yonatan Abrham]

Thanks for your reply Matt. The log file indicates a syntax error.

The content of the log file is the following:

/mnt/2/opt/HCP/HCPpipelines/PreFreeSurfer/PreFreeSurferPipeline.sh
========================================
  DIRECTORY: /opt/HCP/HCPpipelines
    PRODUCT: HCP Pipeline Scripts
    VERSION: v4.4.0-rc-MOD-e7a6af9
     COMMIT: e7a6af936d3a9255a2585d2cc16cdea85454e6ca
   MODIFIED: YES
========================================
Mon May  2 12:14:10 EDT 2022:PreFreeSurferPipeline.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Mon May  2 12:14:10 EDT 2022:PreFreeSurferPipeline.sh: FSLDIR: /opt/fsl/fsl
Mon May  2 12:14:10 EDT 2022:PreFreeSurferPipeline.sh: HCPPIPEDIR_Global: /opt/HCP/HCPpipelines/global/scripts
Mon May  2 12:14:10 EDT 2022:PreFreeSurferPipeline.sh: Platform Information Follows:
Linux bhcr003 3.10.0-1160.6.1.el7.x86_64 #1 SMP Wed Oct 21 13:44:38 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
Mon May  2 12:14:10 EDT 2022:PreFreeSurferPipeline.sh: Parsing Command Line Options
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: Finished Parsing Command Line Options
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: StudyFolder: mnt/0/data/sub-C1052/preprocessed/
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: Subject: sub-C1052
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: T1wInputImages: mnt/0/data/sub-C1052//anat/sub-C1052_run-1_T1w.nii.gz
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: T2wInputImages: mnt/0/data/sub-C1052//anat/sub-C1052_run-1_T2w.nii.gz
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: T1wTemplate: /mnt/2/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.8mm.nii.gz
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: T1wTemplateBrain: /mnt/2/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.8mm_brain.nii.gz
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: T1wTemplate2mm: /mnt/2/opt/HCP/HCPpipelines/global/templates/MNI152_T1_2mm.nii.gz
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: T2wTemplate: /mnt/2/opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.8mm.nii.gz
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: T2wTemplateBrain: /mnt/2/opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.8mm_brain.nii.gz
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: T2wTemplate2mm: /mnt/2/opt/HCP/HCPpipelines/global/templates/MNI152_T2_2mm.nii.gz
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: TemplateMask: /mnt/2/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.8mm_brain_mask.nii.gz
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: Template2mmMask: /mnt/2/opt/HCP/HCPpipelines/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: BrainSize: 150
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: FNIRTConfig: /mnt/2/opt/HCP/HCPpipelines/global/config/T1_2_MNI152_2mm.cnf
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: MagnitudeInputName: NONE
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: PhaseInputName:
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: GEB0InputName:
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: TE:
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: SpinEchoPhaseEncodeNegative: mnt/0/data/sub-C1052//fmap/sub-C1052_dir-AP_run-1_epi.nii.gz
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: SpinEchoPhaseEncodePositive: mnt/0/data/sub-C1052//fmap/sub-C1052_dir-PA_run-1_epi.nii.gz
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: SEEchoSpacing:
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: SEUnwarpDir: y
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: T1wSampleSpacing: 0.0000074
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: T2wSampleSpacing: 0.0000035
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: UnwarpDir: z
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: GradientDistortionCoeffs:
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: AvgrdcSTRING: TOPUP
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: TopupConfig: /opt/HCP/HCPpipelines/global/config/b02b0.cnf
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: BiasFieldSmoothingSigma:
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: UseJacobian: true
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: T1wBiasCorrect:
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: CustomBrain: NONE
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: ProcessingMode: HCPStyleData
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: T1wFolder: mnt/0/data/sub-C1052/preprocessed//sub-C1052/T1w
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: T2wFolder: mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: AtlasSpaceFolder: mnt/0/data/sub-C1052/preprocessed//sub-C1052/MNINonLinear
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: mkdir -p mnt/0/data/sub-C1052/preprocessed//sub-C1052/T1w/xfms/
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: mkdir -p mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w/xfms/
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: mkdir -p mnt/0/data/sub-C1052/preprocessed//sub-C1052/MNINonLinear/xfms/
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: POSIXLY_CORRECT=
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: Processing Modality: T1w
Mon May  2 12:14:11 EDT 2022:PreFreeSurferPipeline.sh: NOT PERFORMING GRADIENT DISTORTION CORRECTION
Mon May  2 12:14:13 EDT 2022:PreFreeSurferPipeline.sh: Not Averaging T1w Images
Mon May  2 12:14:13 EDT 2022:PreFreeSurferPipeline.sh: ONLY ONE IMAGE FOUND: COPYING
Mon May  2 12:14:14 EDT 2022:PreFreeSurferPipeline.sh: Aligning T1w image to /mnt/2/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.8mm.nii.gz to create native volume space
Mon May  2 12:14:14 EDT 2022:PreFreeSurferPipeline.sh: mkdir -p mnt/0/data/sub-C1052/preprocessed//sub-C1052/T1w/ACPCAlignment
Mon May  2 12:14:14 EDT 2022:ACPCAlignment.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Mon May  2 12:14:14 EDT 2022:ACPCAlignment.sh: FSLDIR: /opt/fsl/fsl
Mon May  2 12:14:14 EDT 2022:ACPCAlignment.sh: START
Final FOV is:
0.000000 208.000000 0.000000 300.000000 97.000000 188.000000

Mon May  2 12:15:28 EDT 2022:ACPCAlignment.sh: END
Mon May  2 12:15:28 EDT 2022:PreFreeSurferPipeline.sh: Performing Brain Extraction using FNIRT-based Masking
Mon May  2 12:15:28 EDT 2022:PreFreeSurferPipeline.sh: mkdir -p mnt/0/data/sub-C1052/preprocessed//sub-C1052/T1w/BrainExtraction_FNIRTbased
Mon May  2 12:15:28 EDT 2022:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Mon May  2 12:15:28 EDT 2022:BrainExtraction_FNIRTbased.sh: FSLDIR: /opt/fsl/fsl
Mon May  2 12:15:28 EDT 2022:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR_Templates: /opt/HCP/HCPpipelines/global/templates
Mon May  2 12:15:28 EDT 2022:BrainExtraction_FNIRTbased.sh: START: BrainExtraction_FNIRT
Mon May  2 12:26:41 EDT 2022:BrainExtraction_FNIRTbased.sh: END: BrainExtraction_FNIRT
Mon May  2 12:26:41 EDT 2022:PreFreeSurferPipeline.sh: Processing Modality: T2w
Mon May  2 12:26:41 EDT 2022:PreFreeSurferPipeline.sh: NOT PERFORMING GRADIENT DISTORTION CORRECTION
Mon May  2 12:26:43 EDT 2022:PreFreeSurferPipeline.sh: Not Averaging T2w Images
Mon May  2 12:26:43 EDT 2022:PreFreeSurferPipeline.sh: ONLY ONE IMAGE FOUND: COPYING
Mon May  2 12:26:44 EDT 2022:PreFreeSurferPipeline.sh: Aligning T2w image to /mnt/2/opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.8mm.nii.gz to create native volume space
Mon May  2 12:26:44 EDT 2022:PreFreeSurferPipeline.sh: mkdir -p mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w/ACPCAlignment
Mon May  2 12:26:44 EDT 2022:ACPCAlignment.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Mon May  2 12:26:44 EDT 2022:ACPCAlignment.sh: FSLDIR: /opt/fsl/fsl
Mon May  2 12:26:44 EDT 2022:ACPCAlignment.sh: START
Final FOV is:
0.000000 208.000000 0.000000 300.000000 98.000000 188.000000

Mon May  2 12:28:00 EDT 2022:ACPCAlignment.sh: END
Mon May  2 12:28:00 EDT 2022:PreFreeSurferPipeline.sh: Performing Brain Extraction using FNIRT-based Masking
Mon May  2 12:28:00 EDT 2022:PreFreeSurferPipeline.sh: mkdir -p mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w/BrainExtraction_FNIRTbased
Mon May  2 12:28:00 EDT 2022:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Mon May  2 12:28:00 EDT 2022:BrainExtraction_FNIRTbased.sh: FSLDIR: /opt/fsl/fsl
Mon May  2 12:28:00 EDT 2022:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR_Templates: /opt/HCP/HCPpipelines/global/templates
Mon May  2 12:28:00 EDT 2022:BrainExtraction_FNIRTbased.sh: START: BrainExtraction_FNIRT
Mon May  2 12:39:35 EDT 2022:BrainExtraction_FNIRTbased.sh: END: BrainExtraction_FNIRT
Mon May  2 12:39:35 EDT 2022:PreFreeSurferPipeline.sh: Performing TOPUP Readout Distortion Correction
Mon May  2 12:39:35 EDT 2022:PreFreeSurferPipeline.sh: mkdir -p mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w/T2wToT1wDistortionCorrectAndReg
Mon May  2 12:39:35 EDT 2022:T2wToT1wDistortionCorrectAndReg.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Mon May  2 12:39:35 EDT 2022:T2wToT1wDistortionCorrectAndReg.sh: FSLDIR: /opt/fsl/fsl
Mon May  2 12:39:35 EDT 2022:T2wToT1wDistortionCorrectAndReg.sh: HCPPIPEDIR_Global: /opt/HCP/HCPpipelines/global/scripts
Mon May  2 12:39:36 EDT 2022:T2wToT1wDistortionCorrectAndReg.sh: START
TopupPreprocessingAll.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
TopupPreprocessingAll.sh: FSLDIR: /opt/fsl/fsl
TopupPreprocessingAll.sh: HCPPIPEDIR_Global: /opt/HCP/HCPpipelines/global/scripts
Mon May  2 12:39:36 EDT 2022:TopupPreprocessingAll.sh: START: Topup Field Map Generation and Gradient Unwarping
(standard_in) 1: syntax error

Part of FSL (ID: 6.0.5:9e026117)
topup

Usage:
topup --imain=<some 4D image> --datain=<text file> --config=<text file with parameters> --out=my_topup_results


Compulsory arguments (You MUST set one or more of):
    --imain        name of 4D file with images
    --datain    name of text file with PE directions/times

Optional arguments (You may optionally specify one or more of):
    --out        base-name of output files (spline coefficients (Hz) and movement parameters)
    --fout        name of image file with field (Hz)
    --iout        name of 4D image file with unwarped images
    --logout    Name of log-file
    --warpres    (approximate) resolution (in mm) of warp basis for the different sub-sampling levels, default 10
    --subsamp    sub-sampling scheme, default 1
    --fwhm        FWHM (in mm) of gaussian smoothing kernel, default 8
    --config    Name of config file specifying command line arguments
    --miter        Max # of non-linear iterations, default 5
    --lambda    Weight of regularisation, default depending on --ssqlambda and --regmod switches. See user documetation.
    --ssqlambda    If set (=1), lambda is weighted by current ssq, default 1
    --regmod    Model for regularisation of warp-field [membrane_energy bending_energy], default bending_energy
    --estmov    Estimate movements if set, default 1 (true)
    --minmet    Minimisation method 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient, default 0 (LM)
    --splineorder    Order of spline, 2->Qadratic spline, 3->Cubic spline. Default=3
    --numprec    Precision for representing Hessian, double or float. Default double
    --interp    Image interpolation model, linear or spline. Default spline
    --scale        If set (=1), the images are individually scaled to a common mean, default 0 (false)
    --regrid        If set (=1), the calculations are done in a different grid, default 1 (true)
    -h,--help    display help info
    -v,--verbose    Print diagonostic information while running
    -h,--help    display help info




Mon May  2 12:40:07 EDT 2022:TopupPreprocessingAll.sh: While running '/opt/HCP/HCPpipelines/global/scripts/TopupPreprocessingAll.sh --workingdir=mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap --phaseone=mnt/0/data/sub-C1052//fmap/sub-C1052_dir-AP_run-1_epi.nii.gz --phasetwo=mnt/0/data/sub-C1052//fmap/sub-C1052_dir-PA_run-1_epi.nii.gz --scoutin=mnt/0/data/sub-C1052//fmap/sub-C1052_dir-PA_run-1_epi.nii.gz --echospacing= --unwarpdir=y --ofmapmag=mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w/T2wToT1wDistortionCorrectAndReg/Magnitude --ofmapmagbrain=mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w/T2wToT1wDistortionCorrectAndReg/Magnitude_brain --ofmap=mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap --ojacobian=mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w/T2wToT1wDistortionCorrectAndReg/Jacobian --gdcoeffs= --topupconfig=/opt/HCP/HCPpipelines/global/config/b02b0.cnf --usejacobian=true':
Mon May  2 12:40:07 EDT 2022:TopupPreprocessingAll.sh: ERROR: '/opt/fsl/fsl/bin/topup' command failed with return code: 1
Mon May  2 12:40:07 EDT 2022:TopupPreprocessingAll.sh: ERROR: '/opt/fsl/fsl/bin/topup' command failed with return code: 1

===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
         script: TopupPreprocessingAll.sh
stopped at line: 286
           call: ${FSLDIR}/bin/topup --imain=${WD}/BothPhases --datain=$txtfname --config=${TopupConfig} --out=${WD}/Coefficents --iout=${WD}/Magnitudes --fout=${WD}/TopupField --dfout=${WD}/WarpField --rbmout=${WD}/MotionMatrix --jacout=${WD}/Jacobian -v
  expanded call: /opt/fsl/fsl/bin/topup --imain=mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/BothPhases --datain=mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/acqparams.txt --config=/opt/HCP/HCPpipelines/global/config/b02b0.cnf --out=mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/Coefficents --iout=mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/Magnitudes --fout=mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/TopupField --dfout=mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/WarpField --rbmout=mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/MotionMatrix --jacout=mnt/0/data/sub-C1052/preprocessed//sub-C1052/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/Jacobian -v
      exit code: 1

My script to call PreFreeSurferPipeline.sh is the following:

${HCPPipe}/PreFreeSurfer/PreFreeSurferPipeline.sh \
        --path="${datadir}" \
        --subject="${subj}" \
        --t1="${unprocesseddir}/anat/${subj}_run-1_T1w.nii.gz" \
        --t2="${unprocesseddir}/anat/${subj}_run-1_T2w.nii.gz" \
        --t1template="${t1template}" \
        --t1templatebrain="${t1templatebrain}" \
        --t1template2mm="${t1template2mm}" \
        --t2template="${t2template}" \
        --t2templatebrain="$t2templatebrain" \
        --t2template2mm="$t2template2mm" \
        --templatemask="$templatemask" \
        --template2mmmask="$template2mmmask" \
        --brainsize="${brainsize}" \
        --fmapmag="NONE" \
        --fnirtconfig="${HCPPipe}/global/config/T1_2_MNI152_2mm.cnf" \
        --SEPhaseNeg="${unprocesseddir}/fmap/${subj}_dir-AP_run-1_epi.nii.gz" \
        --SEPhasePos="${unprocesseddir}/fmap/${subj}_dir-PA_run-1_epi.nii.gz" \
        --echospacing="$DwellTime_SE" \
        --seunwarpdir="${seunwarpdir}" \
        --t1samplespacing="$T1wSampleSpacing" \
        --t2samplespacing="$T2wSampleSpacing" \
        --unwarpdir="z" \
        --grdcoeffs="NONE" \
        --avgrdcmethod="TOPUP" \
        --topupconfig="${HCPPIPEDIR_Config}/b02b0.cnf" \
      

Thank you,

Yonatan

[Glasser, Matt]

Whatever you put for $DwellTime_SE didn’t actually make it into your pipeline call.

[Yonatan Abrham]

Thank you very much Matt, so far it didn't crash.

Best,

Yonatan

[Yonatan Abrham]

It was the way I was passing  $DwellTime_SE that was causing the issue.

Thanks again.

Yonatan

[Yonatan Abrham]

Greetings,

I'm facing another issue. It was able to create other files under but Cannot create directory mnt/0/data/sub-C1052/preprocessed//sub-C1052/MNINonLinear/Native/MSMSulc/   but  not  L.logdir++++++++++++++++++++.  What could be causing this error?

terminate called after throwing an instance of 'std::runtime_error'
  what():  Cannot create directory mnt/0/data/sub-C1052/preprocessed//sub-C1052/MNINonLinear/Native/MSMSulc/L.logdir++++++++++++++++++++
/opt/HCP/HCPpipelines/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh: line 295: 46184 Aborted                 (core dumped) ${MSMBINDIR}/msm --conf=${MSMCONFIGDIR}/MSMSulcStrainFinalconf --inmesh="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii --refmesh="$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii --indata="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sulc.native.shape.gii --refdata="$AtlasSpaceFolder"/${Subject}.${Hemisphere}.refsulc."$HighResMesh"k_fs_LR.shape.gii --out="$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}. --verbose
Tue May  3 17:23:24 EDT 2022:FreeSurfer2CaretConvertAndRegisterNonlinear.sh: While running '/opt/HCP/HCPpipelines/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh mnt/0/data/sub-C1052/preprocessed/ sub-C1052 mnt/0/data/sub-C1052/preprocessed//sub-C1052/T1w mnt/0/data/sub-C1052/preprocessed//sub-C1052/MNINonLinear Native mnt/0/data/sub-C1052/preprocessed//sub-C1052/T1w/sub-C1052 T1w_acpc_dc_restore_1mm T1w_acpc_dc_restore T2w_acpc_dc_restore /opt/HCP/HCPpipelines/global/templates/standard_mesh_atlases 164 32 mnt/0/data/sub-C1052/preprocessed//sub-C1052/MNINonLinear/xfms/acpc_dc2standard mnt/0/data/sub-C1052/preprocessed//sub-C1052/MNINonLinear/xfms/standard2acpc_dc T1w_restore T2w_restore brainmask_fs /opt/HCP/HCPpipelines/global/config/FreeSurferAllLut.txt /opt/HCP/HCPpipelines/global/templates/91282_Greyordinates 2 /opt/HCP/HCPpipelines/global/config/FreeSurferSubcorticalLabelTableLut.txt MSMSulc 1':
Tue May  3 17:23:24 EDT 2022:FreeSurfer2CaretConvertAndRegisterNonlinear.sh: ERROR: '/opt/MSM_HOCR_v3/msm' command failed with return code: 134
Tue May  3 17:23:24 EDT 2022:FreeSurfer2CaretConvertAndRegisterNonlinear.sh: ERROR: '/opt/MSM_HOCR_v3/msm' command failed with return code: 134

===> ERROR: Command returned with nonzero exit code
---------------------------------------------------

         script: FreeSurfer2CaretConvertAndRegisterNonlinear.sh
stopped at line: 430
           call: ${MSMBINDIR}/msm --conf=${MSMCONFIGDIR}/MSMSulcStrainFinalconf --inmesh="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii --refmesh="$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii --indata="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sulc.native.shape.gii --refdata="$AtlasSpaceFolder"/${Subject}.${Hemisphere}.refsulc."$HighResMesh"k_fs_LR.shape.gii --out="$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}. --verbose
  expanded call: /opt/MSM_HOCR_v3/msm --conf=/opt/HCP/HCPpipelines/MSMConfig/MSMSulcStrainFinalconf --inmesh=mnt/0/data/sub-C1052/preprocessed//sub-C1052/MNINonLinear/Native/sub-C1052.L.sphere.rot.native.surf.gii --refmesh=mnt/0/data/sub-C1052/preprocessed//sub-C1052/MNINonLinear/sub-C1052.L.sphere.164k_fs_LR.surf.gii --indata=mnt/0/data/sub-C1052/preprocessed//sub-C1052/MNINonLinear/Native/sub-C1052.L.sulc.native.shape.gii --refdata=mnt/0/data/sub-C1052/preprocessed//sub-C1052/MNINonLinear/sub-C1052.L.refsulc.164k_fs_LR.shape.gii --out=mnt/0/data/sub-C1052/preprocessed//sub-C1052/MNINonLinear/Native/MSMSulc/L. --verbose
      exit code: 134
---------------------------------------------------

Thank you,

Yonatan

[Glasser, Matt]

Perhaps there are too many +++.  Perhaps you should start fresh?

Matt.

[Yonatan Abrham]

Thanks Matt. What does ++++ indicate? So, should I delete all of the outputs and rerun the script?

Thank you,

Yonatan

[Glasser, Matt]

It means that you have run it over and over.  Perhaps starting fresh will work.

[Yonatan Abrham]

Thanks Matt, I will try it again.

Best,

Yonatan

[Yonatan Abrham]

I still get the same error after deleting everything and starting all over again. I only ran  PostFreeSurferPipeline.sh once.

Cannot create directory mnt/0/data/sub-C1052/preprocessed//sub-C1052/MNINonLinear/Native/MSMSulc/L.logdir++++++++++++++++++++

Thanks,

Yonatan