DCAN-Labs/abcd-hcp-pipeline

Exception: error caught during stage: DCANBOLDProcessing

Closed this issue · 4 comments

sunlianglong commented

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-A00018030/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 the latest version in https://hub.docker.com/r/dcanumn/abcd-hcp-pipeline .

Looking for your replay!

singularity run -e
-B /HeLabData2/llsun/NKIdataset/BIDS_Test/BIDSData:/bids_input
-B /HeLabData2/llsun/NKIdataset/BIDS_Test/ABCDHCP_Results_CBDPtest:/output
-B /HeLabData2/llsun/NKIdataset/license.txt:/opt/freesurfer/license.txt
/HeLabData2/llsun/tool_packages/Container_Package/abcd-hcp-pipeline.sif
/bids_input /output
--participant-label CBDP0009A
--freesurfer-license=/opt/freesurfer/license.txt --ncpus 8

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

madisoth commented

Hello and thank you for reporting that error-- it is a known issue in the v0.1.1 / "latest" release and we intend to have a fixed version released shortly; apologies for the trouble.

In the meantime, the prior release (v0.1.0) should work. v0.1.1 only changed the included Matlab runtime version (which is the cause of your error), and fixed a bandstop filter bug which wouldn't affect your dataset since you are not using the filter.

Also if you still have the incomplete output, you should be able to run v0.1.0 with --stage DCANBOLDProcessing to resume from where the error was occuring. If with v0.1.0 you still have issues let us know. Thanks!

sunlianglong commented

Hello Madison, thanks ! It worked in the prior release (v0.1.0).

Will the next release in docker hub fix this bug?

arueter1 commented

@sunlianglong - we are checking on when the next docker hub fix is coming. More to come soon. Thanks for your patience!

madisoth commented

Should be resolved as of the latest release (v0.1.3 at this time)