Files missing in different stages of the pipeline

**Hi,

I've been trying to run the nhp-abcd-bids-pipeline for surface reconstruction using Macaque MR images. I have both T1w and T2w images. I have validated the BIDS file structure using the bids-validator.

Result of the bids-validator output**

bids-validator@1.5.2

1: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered based on the presence of only one author field. Please ignore if all contributors are already properly listed. (code: 102 - TOO_FEW_AUTHORS)

Please visit https://neurostars.org/search?q=TOO_FEW_AUTHORS for existing conversations about this issue.

    Summary:                Available Tasks:        Available Modalities: 
    9 Files, 15.33MB                                T1w                   
    1 - Subject                                     T2w                   
    1 - Session                                                           

If you have any questions, please post on https://neurostars.org/tags/bids.

I ran the pipeline using the following command.

sudo docker run --rm -v /media/nipun/Data/Opitz-Lab/Research/TMS-Monkey/MRI/bids-willow:/bids_input:ro -v /media/nipun/Data/Opitz-Lab/Research/TMS-Monkey/MRI/pipeline:/output
-v /usr/local/freesurfer/license.txt:/license dcanlabs/nhp-abcd-bids-pipeline /bids_input /output --freesurfer-license=/license

The resulting console output is as follows.

running PreliminaryMasking /opt/pipeline/PreliminaryMasking/macaque_masking.py \ --path=/output/sub-Willow/ses-None/files \ --t1 \ /bids_input/sub-Willow/anat/sub-Willow_T1w.nii.gz \ --t2 \ /bids_input/sub-Willow/anat/sub-Willow_T2w.nii.gz \ --func= \ --fmapmag=NONE \ --sshead=/opt/pipeline/global/templates/MacaqueYerkes19_T1w_0.5mm.nii.gz \ --ssbrain=/opt/pipeline/global/templates/MacaqueYerkes19_T1w_0.5mm_brain.nii.gz \ --verbose running PreFreeSurfer /opt/pipeline/PreFreeSurfer/PreFreeSurferPipeline.sh \ --path=/output/sub-Willow/ses-None/files \ --subject=Willow \ --t1=/bids_input/sub-Willow/anat/sub-Willow_T1w.nii.gz \ --t2=/bids_input/sub-Willow/anat/sub-Willow_T2w.nii.gz \ --t1template=/opt/pipeline/global/templates/MacaqueYerkes19_T1w_0.5mm.nii.gz \ --t1templatebrain=/opt/pipeline/global/templates/MacaqueYerkes19_T1w_0.5mm_brain.nii.gz \ --t1template2mm=/opt/pipeline/global/templates/MacaqueYerkes19_T1w_1.0mm.nii.gz \ --t2template=/opt/pipeline/global/templates/MacaqueYerkes19_T2w_0.5mm.nii.gz \ --t2templatebrain=/opt/pipeline/global/templates/MacaqueYerkes19_T2w_0.5mm_brain.nii.gz \ --t2template2mm=/opt/pipeline/global/templates/MacaqueYerkes19_T2w_1.0mm.nii.gz \ --templatemask=/opt/pipeline/global/templates/MacaqueYerkes19_T1w_0.5mm_brain_mask.nii.gz \ --template2mmmask=/opt/pipeline/global/templates/MacaqueYerkes19_T1w_1.0mm_brain_mask.nii.gz \ --brainsize=150 \ --fnirtconfig=/opt/pipeline/global/config/T1_2_MNI152_2mm.cnf \ --fmapmag=NONE \ --fmapphase=NONE \ --fmapgeneralelectric=NONE \ --echodiff=NONE \ --SEPhaseNeg=NONE \ --SEPhasePos=NONE \ --echospacing=NONE \ --seunwarpdir=NONE \ --t1samplespacing=0.000015 \ --t2samplespacing=0.0000025 \ --unwarpdir=z- \ --gdcoeffs=NONE \ --avgrdcmethod=NONE \ --topupconfig=/opt/pipeline/global/config/b02b0.cnf \ --useT2=true \ --printcom= \ --fmapmagbrain=NONE \ --revepi=NONE \ --multitemplatedir=NONE found outputs from an earlier run of PreFreeSurfer removing /output/sub-Willow/ses-None/files/T1w/T1w.nii.gz removing /output/sub-Willow/ses-None/files/T1w/T1w_acpc.nii.gz removing /output/sub-Willow/ses-None/files/T1w/xfms/acpc.mat removing /output/sub-Willow/ses-None/files/T1w/T1w_acpc_brain.nii.gz missing expected outputs from PreFreeSurfer file not found: /output/sub-Willow/ses-None/files/T1w/T1w_acpc_brain_mask.nii.gz file not found: /output/sub-Willow/ses-None/files/T1w/T1w_acpc_dc_brain.nii.gz file not found: /output/sub-Willow/ses-None/files/T1w/T1w_acpc_dc_restore.nii.gz file not found: /output/sub-Willow/ses-None/files/T1w/T1w_acpc_dc_restore_brain.nii.gz file not found: /output/sub-Willow/ses-None/files/T1w/BiasField_acpc_dc.nii.gz running FreeSurfer /opt/pipeline/FreeSurfer/FreeGreyPipeline.sh \ --subject=Willow \ --subjectDIR=/output/sub-Willow/ses-None/files/T1w \ --t1=/output/sub-Willow/ses-None/files/T1w/T1w_acpc_dc_restore.nii.gz \ --t1brain=/output/sub-Willow/ses-None/files/T1w/T1w_acpc_dc_restore_brain.nii.gz \ --t2=/output/sub-Willow/ses-None/files/T1w/T2w_acpc_dc_restore.nii.gz \ --normalizationMethod=ADULT_GM_IP \ --useT2=true \ --aseg=/output/sub-Willow/ses-None/files/T1w/aseg_acpc.nii.gz \ --gca=/opt/pipeline/global/templates/MacaqueYerkes19/RB_all_2008-03-26.gca \ --maxThickness=5 \ --printcom= missing expected outputs from FreeSurfer file not found: /output/sub-Willow/ses-None/files/T1w/T1w_acpc_dc_restore_brain_1mm.nii.gz file not found: /output/sub-Willow/ses-None/files/T1w/Willow/label/lh.aparc.a2009s.annot file not found: /output/sub-Willow/ses-None/files/T1w/Willow/label/lh.aparc.annot file not found: /output/sub-Willow/ses-None/files/T1w/Willow/label/rh.aparc.annot file not found: /output/sub-Willow/ses-None/files/T1w/Willow/surf/lh.pial file not found: /output/sub-Willow/ses-None/files/T1w/Willow/surf/lh.sphere file not found: /output/sub-Willow/ses-None/files/T1w/Willow/surf/lh.sphere.reg file not found: /output/sub-Willow/ses-None/files/T1w/Willow/surf/lh.white file not found: /output/sub-Willow/ses-None/files/T1w/Willow/surf/rh.pial file not found: /output/sub-Willow/ses-None/files/T1w/Willow/surf/rh.sphere file not found: /output/sub-Willow/ses-None/files/T1w/Willow/surf/rh.sphere.reg file not found: /output/sub-Willow/ses-None/files/T1w/Willow/surf/rh.white running PostFreeSurfer /opt/pipeline/PostFreeSurfer/PostFreeSurferPipeline.sh \ --path=/output/sub-Willow/ses-None/files \ --subject=Willow \ --surfatlasdir=/opt/pipeline/global/templates/standard_mesh_atlases \ --grayordinatesdir=/opt/pipeline/global/templates/91282_Greyordinates \ --grayordinatesres=1.25 \ --hiresmesh=164 \ --lowresmesh=32 \ --subcortgraylabels=/opt/pipeline/global/config/FreeSurferSubcorticalLabelTableLut.txt \ --freesurferlabels=/opt/pipeline/global/config/FreeSurferAllLut.txt \ --refmyelinmaps=/opt/pipeline/global/templates/standard_mesh_atlases/MacaqueYerkes19.MyelinMap_BC.164k_fs_LR.dscalar.nii \ --regname=FS \ --reference2mm=/opt/pipeline/global/templates/MacaqueYerkes19_T1w_1.0mm.nii.gz \ --reference2mmmask=/opt/pipeline/global/templates/MacaqueYerkes19_T1w_1.0mm_brain_mask.nii.gz \ --config=/opt/pipeline/global/config/T1_2_MNI152_2mm.cnf \ --useT2=true \ --t1template=/opt/pipeline/global/templates/MacaqueYerkes19_T1w_0.5mm.nii.gz \ --t1templatebrain=/opt/pipeline/global/templates/MacaqueYerkes19_T1w_0.5mm_brain.nii.gz \ --t1template2mm=/opt/pipeline/global/templates/MacaqueYerkes19_T1w_1.0mm.nii.gz \ --t2template=/opt/pipeline/global/templates/MacaqueYerkes19_T2w_0.5mm.nii.gz \ --t2templatebrain=/opt/pipeline/global/templates/MacaqueYerkes19_T2w_0.5mm_brain.nii.gz \ --t2template2mm=/opt/pipeline/global/templates/MacaqueYerkes19_T2w_1.0mm.nii.gz \ --templatemask=/opt/pipeline/global/templates/MacaqueYerkes19_T1w_0.5mm_brain_mask.nii.gz \ --template2mmmask=/opt/pipeline/global/templates/MacaqueYerkes19_T1w_1.0mm_brain_mask.nii.gz \ --printcom= found outputs from an earlier run of PostFreeSurfer removing /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage/Willow.L.def_sphere.164k_fs_L.surf.gii removing /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage/Willow.L.sphere.164k_fs_L.surf.gii removing /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage/Willow.R.def_sphere.164k_fs_R.surf.gii removing /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage/Willow.R.sphere.164k_fs_R.surf.gii removing /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.L.atlasroi.32k_fs_LR.shape.gii removing /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.L.sphere.32k_fs_LR.surf.gii removing /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.R.atlasroi.32k_fs_LR.shape.gii removing /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.R.sphere.32k_fs_LR.surf.gii removing /output/sub-Willow/ses-None/files/MNINonLinear/Willow.164k_fs_LR.wb.spec removing /output/sub-Willow/ses-None/files/MNINonLinear/Willow.L.atlasroi.164k_fs_LR.shape.gii removing /output/sub-Willow/ses-None/files/MNINonLinear/Willow.L.refsulc.164k_fs_LR.shape.gii removing /output/sub-Willow/ses-None/files/MNINonLinear/Willow.L.sphere.164k_fs_LR.surf.gii removing /output/sub-Willow/ses-None/files/MNINonLinear/Willow.R.atlasroi.164k_fs_LR.shape.gii removing /output/sub-Willow/ses-None/files/MNINonLinear/Willow.R.refsulc.164k_fs_LR.shape.gii removing /output/sub-Willow/ses-None/files/MNINonLinear/Willow.R.sphere.164k_fs_LR.surf.gii missing expected outputs from PostFreeSurfer file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.ArealDistortion_FS.native.dscalar.nii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.L.aparc.a2009s.native.label.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.L.aparc.native.label.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.L.atlasroi.native.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.L.curvature.native.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.L.inflated.native.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.L.midthickness.native.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.L.pial.native.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.L.roi.native.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.L.sphere.native.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.L.sphere.reg.native.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.L.sphere.reg.reg_LR.native.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.L.sulc.native.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.L.thickness.native.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.L.very_inflated.native.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.L.white.native.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.R.aparc.a2009s.native.label.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.R.aparc.native.label.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.R.atlasroi.native.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.R.curvature.native.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.R.inflated.native.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.R.midthickness.native.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.R.pial.native.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.R.roi.native.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.R.sphere.native.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.R.sphere.reg.native.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.R.sphere.reg.reg_LR.native.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.R.sulc.native.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.R.thickness.native.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.R.very_inflated.native.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.R.white.native.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.aparc.a2009s.native.dlabel.nii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.aparc.native.dlabel.nii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.curvature.native.dscalar.nii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.native.wb.spec file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.sulc.native.dscalar.nii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Native/Willow.thickness.native.dscalar.nii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/aparc+aseg.nii.gz file not found: /output/sub-Willow/ses-None/files/MNINonLinear/aparc.a2009s+aseg.nii.gz file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.ArealDistortion_FS.32k_fs_LR.dscalar.nii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.L.ArealDistortion_FS.32k_fs_LR.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.L.aparc.32k_fs_LR.label.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.L.aparc.a2009s.32k_fs_LR.label.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.L.curvature.32k_fs_LR.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.L.inflated.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.L.midthickness.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.L.pial.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.L.sulc.32k_fs_LR.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.L.thickness.32k_fs_LR.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.L.very_inflated.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.L.white.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.R.ArealDistortion_FS.32k_fs_LR.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.R.aparc.32k_fs_LR.label.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.R.aparc.a2009s.32k_fs_LR.label.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.R.curvature.32k_fs_LR.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.R.inflated.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.R.midthickness.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.R.pial.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.R.sulc.32k_fs_LR.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.R.thickness.32k_fs_LR.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.R.very_inflated.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.R.white.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.aparc.32k_fs_LR.dlabel.nii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.aparc.a2009s.32k_fs_LR.dlabel.nii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.curvature.32k_fs_LR.dscalar.nii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.sulc.32k_fs_LR.dscalar.nii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/fsaverage_LR32k/Willow.thickness.32k_fs_LR.dscalar.nii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/ribbon.nii.gz file not found: /output/sub-Willow/ses-None/files/MNINonLinear/wmparc.nii.gz file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.L.ArealDistortion_FS.164k_fs_LR.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.L.aparc.164k_fs_LR.label.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.L.aparc.a2009s.164k_fs_LR.label.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.L.curvature.164k_fs_LR.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.L.inflated.164k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.L.midthickness.164k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.L.pial.164k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.L.sulc.164k_fs_LR.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.L.thickness.164k_fs_LR.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.L.very_inflated.164k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.L.white.164k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.R.ArealDistortion_FS.164k_fs_LR.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.R.aparc.164k_fs_LR.label.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.R.aparc.a2009s.164k_fs_LR.label.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.R.curvature.164k_fs_LR.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.R.inflated.164k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.R.midthickness.164k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.R.pial.164k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.R.sulc.164k_fs_LR.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.R.thickness.164k_fs_LR.shape.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.R.very_inflated.164k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.R.white.164k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.aparc.164k_fs_LR.dlabel.nii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.aparc.a2009s.164k_fs_LR.dlabel.nii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.curvature.164k_fs_LR.dscalar.nii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.sulc.164k_fs_LR.dscalar.nii file not found: /output/sub-Willow/ses-None/files/MNINonLinear/Willow.thickness.164k_fs_LR.dscalar.nii file not found: /output/sub-Willow/ses-None/files/T1w/Native/Willow.L.inflated.native.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/Native/Willow.L.midthickness.native.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/Native/Willow.L.pial.native.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/Native/Willow.L.very_inflated.native.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/Native/Willow.L.white.native.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/Native/Willow.R.inflated.native.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/Native/Willow.R.midthickness.native.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/Native/Willow.R.pial.native.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/Native/Willow.R.very_inflated.native.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/Native/Willow.R.white.native.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/Native/Willow.native.wb.spec file not found: /output/sub-Willow/ses-None/files/T1w/aparc+aseg.nii.gz file not found: /output/sub-Willow/ses-None/files/T1w/aparc+aseg_1mm.nii.gz file not found: /output/sub-Willow/ses-None/files/T1w/aparc.a2009s+aseg.nii.gz file not found: /output/sub-Willow/ses-None/files/T1w/aparc.a2009s+aseg_1mm.nii.gz file not found: /output/sub-Willow/ses-None/files/T1w/brainmask_fs_1mm.nii.gz file not found: /output/sub-Willow/ses-None/files/T1w/fsaverage_LR32k/Willow.32k_fs_LR.wb.spec file not found: /output/sub-Willow/ses-None/files/T1w/fsaverage_LR32k/Willow.L.inflated.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/fsaverage_LR32k/Willow.L.midthickness.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/fsaverage_LR32k/Willow.L.pial.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/fsaverage_LR32k/Willow.L.very_inflated.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/fsaverage_LR32k/Willow.L.white.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/fsaverage_LR32k/Willow.R.inflated.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/fsaverage_LR32k/Willow.R.midthickness.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/fsaverage_LR32k/Willow.R.pial.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/fsaverage_LR32k/Willow.R.very_inflated.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/fsaverage_LR32k/Willow.R.white.32k_fs_LR.surf.gii file not found: /output/sub-Willow/ses-None/files/T1w/ribbon.nii.gz file not found: /output/sub-Willow/ses-None/files/T1w/wmparc.nii.gz file not found: /output/sub-Willow/ses-None/files/T1w/wmparc_1mm.nii.gz Traceback (most recent call last): File "/app/run.py", line 334, in _cli() File "/app/run.py", line 58, in _cli args.freesurfer_license) File "/app/run.py", line 330, in interface stage.run(ncpus) File "/app/pipelines.py", line 579, in run self.teardown(result) File "/app/pipelines.py", line 523, in teardown self.class.name) Exception: error caught during stage: PostFreeSurfer

I appreciate if you could help me with this. Thank you

DCAN-Labs / nhp-abcd-bids-pipeline

Files missing in different stages of the pipeline #7

Result of the bids-validator output**

I ran the pipeline using the following command.