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Washington-University / HCPpipelines

Processing pipelines for the HCP
https://www.humanconnectome.org/
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a error #301

Closed RuiWang0805 closed 4 days ago

RuiWang0805 commented 6 days ago 
Image Exception : #63 :: No image files match: NONE
terminate called after throwing an instance of 'std::runtime_error'
  what():  No image files match: NONE
/home/qwbrain/HCPpipelines/global/scripts/FieldMapPreprocessingAll.sh: line 165: 18644 Aborted                 (core dumped) ${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean ${WD}/Magnitude
Tue Sep 24 00:58:40 CST 2024:FieldMapPreprocessingAll.sh: While running '/home/qwbrain/HCPpipelines/global/scripts/FieldMapPreprocessingAll.sh --workingdir=/home/qwbrain/projects/Pipelines_ExampleData/100307/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap --method=SiemensFieldMap --fmapmag=NONE --fmapphase=NONE --echodiff=NONE --ofmapmag=/home/qwbrain/projects/Pipelines_ExampleData/100307/T2w/T2wToT1wDistortionCorrectAndReg/Magnitude --ofmapmagbrain=/home/qwbrain/projects/Pipelines_ExampleData/100307/T2w/T2wToT1wDistortionCorrectAndReg/Magnitude_brain --ofmap=/home/qwbrain/projects/Pipelines_ExampleData/100307/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap --gdcoeffs=NONE':
Tue Sep 24 00:58:40 CST 2024:FieldMapPreprocessingAll.sh: ERROR: '/home/qwbrain/fsl/bin/fslmaths' command failed with return code: 134

===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
         script: FieldMapPreprocessingAll.sh
stopped at line: 173
           call: ${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean ${WD}/Magnitude
  expanded call: /home/qwbrain/fsl/bin/fslmaths NONE -Tmean /home/qwbrain/projects/Pipelines_ExampleData/100307/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/Magnitude
       hostname: ubuntu
      exit code: 134
---------------------------------------------------

===> Aborting execution!

Tue Sep 24 00:58:40 CST 2024:T2wToT1wDistortionCorrectAndReg.sh: While running '/home/qwbrain/HCPpipelines/PreFreeSurfer/scripts/T2wToT1wDistortionCorrectAndReg.sh --workingdir=/home/qwbrain/projects/Pipelines_ExampleData/100307/T2w/T2wToT1wDistortionCorrectAndReg --t1=/home/qwbrain/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc --t1brain=/home/qwbrain/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_brain --t2=/home/qwbrain/projects/Pipelines_ExampleData/100307/T2w/T2w_acpc --t2brain=/home/qwbrain/projects/Pipelines_ExampleData/100307/T2w/T2w_acpc_brain --fmapmag=NONE --fmapphase=NONE --fmapcombined=NONE --echodiff=NONE --SEPhaseNeg=NONE --SEPhasePos=NONE --seechospacing=NONE --seunwarpdir=NONE --t1sampspacing=0.0000074 --t2sampspacing=0.0000021 --unwarpdir=z --ot1=/home/qwbrain/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc --ot1brain=/home/qwbrain/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_brain --ot1warp=/home/qwbrain/projects/Pipelines_ExampleData/100307/T1w/xfms/T1w_dc --ot2=/home/qwbrain/projects/Pipelines_ExampleData/100307/T1w/T2w_acpc_dc --ot2warp=/home/qwbrain/projects/Pipelines_ExampleData/100307/T1w/xfms/T2w_reg_dc --method=SiemensFieldMap --topupconfig=NONE --gdcoeffs=NONE --usejacobian=1':
Tue Sep 24 00:58:40 CST 2024:T2wToT1wDistortionCorrectAndReg.sh: ERROR: '/home/qwbrain/HCPpipelines/global/scripts/FieldMapPreprocessingAll.sh' command failed with return code: 134

===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
         script: T2wToT1wDistortionCorrectAndReg.sh
stopped at line: 222
           call: ${HCPPIPEDIR_Global}/FieldMapPreprocessingAll.sh --workingdir=${WD}/FieldMap --method="SiemensFieldMap" --fmapmag=${MagnitudeInputName} --fmapphase=${PhaseInputName} --echodiff=${DeltaTE} --ofmapmag=${WD}/Magnitude --ofmapmagbrain=${WD}/Magnitude_brain --ofmap=${WD}/FieldMap --gdcoeffs=${GradientDistortionCoeffs}
  expanded call: /home/qwbrain/HCPpipelines/global/scripts/FieldMapPreprocessingAll.sh --workingdir=/home/qwbrain/projects/Pipelines_ExampleData/100307/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap --method=SiemensFieldMap --fmapmag=NONE --fmapphase=NONE --echodiff=NONE --ofmapmag=/home/qwbrain/projects/Pipelines_ExampleData/100307/T2w/T2wToT1wDistortionCorrectAndReg/Magnitude --ofmapmagbrain=/home/qwbrain/projects/Pipelines_ExampleData/100307/T2w/T2wToT1wDistortionCorrectAndReg/Magnitude_brain --ofmap=/home/qwbrain/projects/Pipelines_ExampleData/100307/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap --gdcoeffs=NONE
       hostname: ubuntu
      exit code: 134
---------------------------------------------------

===> Aborting execution!

Tue Sep 24 00:58:41 CST 2024:PreFreeSurferPipeline.sh: While running '/home/qwbrain/HCPpipelines/PreFreeSurfer/PreFreeSurferPipeline.sh --path=/home/qwbrain/projects/Pipelines_ExampleData --subject=100307 --t1=/home/qwbrain/projects/Pipelines_ExampleData/100307/unprocessed/3T/T1w_MPR1/100307_3T_T1w_MPR1.nii.gz@ --t2=/home/qwbrain/projects/Pipelines_ExampleData/100307/unprocessed/3T/T2w_SPC1/100307_3T_T2w_SPC1.nii.gz@ --t1template=/home/qwbrain/HCPpipelines/global/templates/MNI152_T1_0.7mm.nii.gz --t1templatebrain=/home/qwbrain/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain.nii.gz --t1template2mm=/home/qwbrain/HCPpipelines/global/templates/MNI152_T1_2mm.nii.gz --t2template=/home/qwbrain/HCPpipelines/global/templates/MNI152_T2_0.7mm.nii.gz --t2templatebrain=/home/qwbrain/HCPpipelines/global/templates/MNI152_T2_0.7mm_brain.nii.gz --t2template2mm=/home/qwbrain/HCPpipelines/global/templates/MNI152_T2_2mm.nii.gz --templatemask=/home/qwbrain/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz --template2mmmask=/home/qwbrain/HCPpipelines/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz --brainsize=150 --fnirtconfig=/home/qwbrain/HCPpipelines/global/config/T1_2_MNI152_2mm.cnf --fmapmag=NONE --fmapphase=NONE --fmapcombined=NONE --echodiff=NONE --SEPhaseNeg=NONE --SEPhasePos=NONE --seechospacing=NONE --seunwarpdir=NONE --t1samplespacing=0.0000074 --t2samplespacing=0.0000021 --unwarpdir=z --gdcoeffs=NONE --avgrdcmethod=SiemensFieldMap --topupconfig=NONE':
Tue Sep 24 00:58:41 CST 2024:PreFreeSurferPipeline.sh: ERROR: '' command failed with return code: 134

===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
         script: PreFreeSurferPipeline.sh
stopped at line: 548
           call: ${RUN} ${HCPPIPEDIR_PreFS}/T2wToT1wDistortionCorrectAndReg.sh --workingdir=${wdir} --t1=${T1wFolder}/${T1wImage}_acpc --t1brain=${T1wFolder}/${T1wImage}_acpc_brain --t2=${T2wFolder_T2wImageWithPath_acpc} --t2brain=${T2wFolder_T2wImageWithPath_acpc_brain} --fmapmag=${MagnitudeInputName} --fmapphase=${PhaseInputName} --fmapcombined=${GEB0InputName} --echodiff=${TE} --SEPhaseNeg=${SpinEchoPhaseEncodeNegative} --SEPhasePos=${SpinEchoPhaseEncodePositive} --seechospacing=${SEEchoSpacing} --seunwarpdir=${SEUnwarpDir} --t1sampspacing=${T1wSampleSpacing} --t2sampspacing=${T2wSampleSpacing} --unwarpdir=${UnwarpDir} --ot1=${T1wFolder}/${T1wImage}_acpc_dc --ot1brain=${T1wFolder}/${T1wImage}_acpc_dc_brain --ot1warp=${T1wFolder}/xfms/${T1wImage}_dc --ot2=${T1wFolder}/${T2wImage}_acpc_dc --ot2warp=${T1wFolder}/xfms/${T2wImage}_reg_dc --method=${AvgrdcSTRING} --topupconfig=${TopupConfig} --gdcoeffs=${GradientDistortionCoeffs} --usejacobian=${UseJacobian}
  expanded call: /home/qwbrain/HCPpipelines/PreFreeSurfer/scripts/T2wToT1wDistortionCorrectAndReg.sh --workingdir=/home/qwbrain/projects/Pipelines_ExampleData/100307/T2w/T2wToT1wDistortionCorrectAndReg --t1=/home/qwbrain/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc --t1brain=/home/qwbrain/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_brain --t2=/home/qwbrain/projects/Pipelines_ExampleData/100307/T2w/T2w_acpc --t2brain=/home/qwbrain/projects/Pipelines_ExampleData/100307/T2w/T2w_acpc_brain --fmapmag=NONE --fmapphase=NONE --fmapcombined=NONE --echodiff=NONE --SEPhaseNeg=NONE --SEPhasePos=NONE --seechospacing=NONE --seunwarpdir=NONE --t1sampspacing=0.0000074 --t2sampspacing=0.0000021 --unwarpdir=z --ot1=/home/qwbrain/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc --ot1brain=/home/qwbrain/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_brain --ot1warp=/home/qwbrain/projects/Pipelines_ExampleData/100307/T1w/xfms/T1w_dc --ot2=/home/qwbrain/projects/Pipelines_ExampleData/100307/T1w/T2w_acpc_dc --ot2warp=/home/qwbrain/projects/Pipelines_ExampleData/100307/T1w/xfms/T2w_reg_dc --method=SiemensFieldMap --topupconfig=NONE --gdcoeffs=NONE --usejacobian=1
       hostname: ubuntu
      exit code: 134
---------------------------------------------------

===> Aborting execution!
glasserm commented 6 days ago

You asked for a fieldmap correction but did not specify the fieldmap magnitude and phase.

RuiWang0805 commented 4 days ago

You asked for a fieldmap correction but did not specify the fieldmap magnitude and phase.

Thanks for your attention and help! I have finished this step Thanks!