Dear all,
when I used the ABCD-HCP pipeline to preprocess two example subjects MRI data (HCP-style MRI for one subject, with fieldmap and T2w image; non HCP-style MRI without fieldmap and T2w for another), I got the same error during the running DCANBOLDProcessing step.
The error is “Exception: error caught during stage: DCANBOLDProcessing”.
I check the logs, I find "FileNotFoundError: [Errno 2] No such file or directory: ‘/output/sub-CBDP0009A/ses-BAS1/files/MNINonLinear/Results/ses-BAS1_task-rest_run-01/DCANBOLDProc_v4.0.0/ses-BAS1_task-rest_run-01_DCANBOLDProc_v4.0.0_Atlas.dtseries.nii’ " in DCANBOLDProcessing_teardown.err and "/opt/dcan-tools/dcan_bold_proc/bin/dcan_signal_processsing: error while loading shared libraries: libmwmclmcrrt.so.9.2: cannot open shared object file: No such file or directory " in ses-BAS1_task-rest_run-01.err .
by the way, the docker file is from the latest version in Docker Hub .
My command is:
singularity run -e
-B /XXXX/BIDS_Test/BIDSData:/bids_input
-B /XXXX/BIDS_Test/ABCDHCP_Results_CBDPtest:/output
-B /XXXX/license.txt:/opt/freesurfer/license.txt
/XXXX/Container_Package/abcd-hcp-pipeline.sif
/bids_input /output
--participant-label CBDP0009A
--freesurfer-license=/opt/freesurfer/license.txt --ncpus 8
And the logs is as follows. All is OK until the DCANBOLDProcessing step.
The pipeline must choose distortion correction method based on the
type(s) of field maps available. The type of fieldmaps you have are
either not able to be used in the abcd-hcp-pipeline or they are
not properly identified in the BIDS format. The pipeline does not
account for ‘phasediff’, ‘magnitude’, and ‘fieldmap’ field maps
filetypes yet. If you have ‘phasediff’ and ‘magnitude’ field maps,
please provide the original ‘phase1’, ‘phase2’, ‘magnitude1’, and
‘magnitude2’ field maps used to calculate those files. The pipeline
does the calculation itself.
running PreFreeSurfer
/opt/pipeline/PreFreeSurfer/PreFreeSurferPipeline.sh
–path=/output/sub-CBDP0009A/ses-None/files
–subject=CBDP0009A
–t1=/bids_input/sub-CBDP0009A/anat/sub-CBDP0009A_T1w.nii.gz
–t2=/bids_input/sub-CBDP0009A/anat/sub-CBDP0009A_T2w.nii.gz
–t1template=/opt/pipeline/global/templates/MNI152_T1_1mm.nii.gz
–t1templatebrain=/opt/pipeline/global/templates/MNI152_T1_1mm_brain.nii.gz
–t1template2mm=/opt/pipeline/global/templates/MNI152_T1_2mm.nii.gz
–t2template=/opt/pipeline/global/templates/MNI152_T2_1mm.nii.gz
–t2templatebrain=/opt/pipeline/global/templates/MNI152_T2_1mm_brain.nii.gz
–t2template2mm=/opt/pipeline/global/templates/MNI152_T2_2mm.nii.gz
–templatemask=/opt/pipeline/global/templates/MNI152_T1_1mm_brain_mask.nii.gz
–template2mmmask=/opt/pipeline/global/templates/MNI152_T1_2mm_brain_mask_dil.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=0.000009301
–t2samplespacing=0.000002097
–unwarpdir=z
–gdcoeffs=NONE
–avgrdcmethod=NONE
–topupconfig=/opt/pipeline/global/config/b02b0.cnf
–useT2=true
–printcom=
–useStudyTemplate=false
–StudyTemplate=NONE
–StudyTemplateBrain=NONE
running FreeSurfer
/opt/pipeline/FreeSurfer/FreeSurferPipeline.sh
–subject=CBDP0009A
–subjectDIR=/output/sub-CBDP0009A/ses-None/files/T1w
–t1=/output/sub-CBDP0009A/ses-None/files/T1w/T1w_acpc_dc_restore.nii.gz
–t1brain=/output/sub-CBDP0009A/ses-None/files/T1w/T1w_acpc_dc_restore_brain.nii.gz
–t2=/output/sub-CBDP0009A/ses-None/files/T1w/T2w_acpc_dc_restore.nii.gz
–useT2=true
–printcom=
running PostFreeSurfer
/opt/pipeline/PostFreeSurfer/PostFreeSurferPipeline.sh
–path=/output/sub-CBDP0009A/ses-None/files
–subject=CBDP0009A
–surfatlasdir=/opt/pipeline/global/templates/standard_mesh_atlases
–grayordinatesdir=/opt/pipeline/global/templates/91282_Greyordinates
–grayordinatesres=2
–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/Conte69.MyelinMap_BC.164k_fs_LR.dscalar.nii
–regname=MSMSulc
–reference2mm=/opt/pipeline/global/templates/MNI152_T1_2mm.nii.gz
–reference2mmmask=/opt/pipeline/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz
–config=/opt/pipeline/global/config/T1_2_MNI152_2mm.cnf
–useT2=true
–t1template=/opt/pipeline/global/templates/MNI152_T1_1mm.nii.gz
–t1templatebrain=/opt/pipeline/global/templates/MNI152_T1_1mm_brain.nii.gz
–t1template2mm=/opt/pipeline/global/templates/MNI152_T1_2mm.nii.gz
–t2template=/opt/pipeline/global/templates/MNI152_T2_1mm.nii.gz
–t2templatebrain=/opt/pipeline/global/templates/MNI152_T2_1mm_brain.nii.gz
–t2template2mm=/opt/pipeline/global/templates/MNI152_T2_2mm.nii.gz
–templatemask=/opt/pipeline/global/templates/MNI152_T1_1mm_brain_mask.nii.gz
–template2mmmask=/opt/pipeline/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz
–useStudyTemplate=false
–printcom=
running FMRIVolume
/opt/pipeline/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh
–path=/output/sub-CBDP0009A/ses-None/files
–subject=CBDP0009A
–fmriname=task-rest_run-1
–fmritcs=/bids_input/sub-CBDP0009A/func/sub-CBDP0009A_task-rest_run-1_bold.nii.gz
–fmriscout=NONE
–SEPhaseNeg=NONE
–SEPhasePos=NONE
–fmapmag=NONE
–fmapphase=NONE
–fmapgeneralelectric=NONE
–echospacing=NONE
–echodiff=NONE
–unwarpdir=NONE
–fmrires=2.0
–dcmethod=NONE
–gdcoeffs=NONE
–topupconfig=/opt/pipeline/global/config/b02b0.cnf
–printcom=
–biascorrection=NONE
–mctype=MCFLIRT
–useT2=true
running FMRISurface
/opt/pipeline/fMRISurface/GenericfMRISurfaceProcessingPipeline.sh
–path=/output/sub-CBDP0009A/ses-None/files
–subject=CBDP0009A
–fmriname=task-rest_run-1
–lowresmesh=32
–fmrires=2.0
–smoothingFWHM=2
–grayordinatesres=2
–regname=MSMSulc
running DCANBOLDProcessing
/opt/dcan-tools/dcan_bold_proc/dcan_bold_proc.py
–subject=CBDP0009A
–output-folder=/output/sub-CBDP0009A/ses-None/files
–task=task-rest_run-1
–fd-threshold=0.3
–filter-order=2
–lower-bpf=0.009
–upper-bpf=0.08
–motion-filter-type=notch
–physio=None
–motion-filter-option=5
–motion-filter-order=4
–band-stop-min=None
–band-stop-max=None
–brain-radius=50
–skip-seconds=5
–contiguous-frames=5
Traceback (most recent call last):
File “/app/run.py”, line 374, in
_cli()
File “/app/run.py”, line 68, in _cli
return interface(**kwargs)
File “/app/run.py”, line 370, in interface
stage.run(ncpus)
File “/app/pipelines.py”, line 588, in run
self.teardown(result)
File “/app/pipelines.py”, line 941, in teardown
super(class, self).teardown(result)
File “/app/pipelines.py”, line 534, in teardown
self.class.name)
Exception: error caught during stage: DCANBOLDProcessing