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DCAN-Labs / abcd-hcp-pipeline

bids application for processing functional MRI data, robust to scanner, acquisition and age variability.
https://hub.docker.com/r/dcanumn/abcd-hcp-pipeline
BSD 3-Clause "New" or "Revised" License
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Exception: error caught during stage: FMRIVolume #90

Closed fpichardo-umn closed 1 year ago

fpichardo-umn commented 1 year ago

I got the error in the title while running the pipeline. It seemed to get through the FreeSurfer processing well, but it had an error during the resting-state fMRI processing. I'm unsure what the error is or what to do.

Below, I am including the relevant messages made by the pipeline and the structure of my dataset. I am running this with singularity.

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This is the last command to run: /opt/pipeline/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh \ --path=/output/sub-001/ses-06/files \ --subject=001 \ --fmriname=ses-06_task-rest_run-01 \ --fmritcs=/bids_input/sub-001/ses-06/func/sub-001_ses-06_task-rest_bold.nii.gz \ --fmriscout=NONE \ --SEPhaseNeg=/bids_input/sub-001/ses-06/fmap/sub-001_ses-06_acq-rest_dir-AP_epi.nii.gz \ --SEPhasePos=/bids_input/sub-001/ses-06/fmap/sub-001_ses-06_acq-rest_dir-PA_epi.nii.gz \ --fmapmag=NONE \ --fmapphase=NONE \ --fmapgeneralelectric=NONE \ --echospacing=0.000659995 \ --echodiff=NONE \ --unwarpdir=y \ --fmrires=2.0 \ --dcmethod=TOPUP \ --gdcoeffs=NONE \ --topupconfig=/opt/pipeline/global/config/b02b0.cnf \ --printcom= \ --biascorrection=NONE \ --mctype=MCFLIRT \ --useT2=false

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Error message: Traceback (most recent call last): File "/app/run.py", line 397, in _cli() File "/app/run.py", line 69, in _cli return interface(**kwargs) File "/app/run.py", line 393, in interface stage.run(ncpus) File "/app/pipelines.py", line 592, in run self.teardown(result) File "/app/pipelines.py", line 538, in teardown self.class.name) Exception: error caught during stage: FMRIVolume

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Tail output from logs/FMRIVolume/ses-06_task-rest_run-01.out: START: OneStepResampling

END: OneStepResampling Tue Apr 18 14:47:28 CDT 2023 - GenericfMRIVolumeProcessingPipeline.sh - mkdir -p /output/sub-001/ses-06/files/MNINonLinear/Results/ses-06_task-rest_run-01 Tue Apr 18 14:48:06 CDT 2023 - GenericfMRIVolumeProcessingPipeline.sh - Intensity Normalization and Bias Removal

START: IntensityNormalization

END: IntensityNormalization Tue Apr 18 14:48:58 CDT 2023 - GenericfMRIVolumeProcessingPipeline.sh - Completed

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However, the logs/FMRIVolume/ses-06_task-rest_run-01.err file was empty.

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There was an error in the hariri task that did not break the processing, but we're uninterested in analyzing that data. This error occurred before the above relevant errors.

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The directory structure for my dataset: sub-001 sub-001/ses-06 sub-001/ses-06/anat sub-001/ses-06/anat/sub-001_ses-06_T1w.json sub-001/ses-06/anat/sub-001_ses-06_T1w.nii.gz sub-001/ses-06/dwi sub-001/ses-06/dwi/sub-001_ses-06_dir-PA_dwi.bval sub-001/ses-06/dwi/sub-001_ses-06_dir-PA_dwi.json sub-001/ses-06/dwi/sub-001_ses-06_dir-AP_dwi.bval sub-001/ses-06/dwi/sub-001_ses-06_dir-AP_dwi.bvec sub-001/ses-06/dwi/sub-001_ses-06_dir-AP_dwi.json sub-001/ses-06/dwi/sub-001_ses-06_dir-PA_dwi.bvec sub-001/ses-06/dwi/sub-001_ses-06_dir-PA_dwi.nii.gz sub-001/ses-06/dwi/sub-001_ses-06_dir-AP_dwi.nii.gz sub-001/ses-06/fmap sub-001/ses-06/fmap/sub-001_ses-06_acq-rest_dir-AP_epi.json sub-001/ses-06/fmap/sub-001_ses-06_acq-rest_dir-PA_epi.json sub-001/ses-06/fmap/sub-001_ses-06_acq-hariri_dir-AP_epi.json sub-001/ses-06/fmap/sub-001_ses-06_acq-hariri_dir-AP_epi.nii.gz sub-001/ses-06/fmap/sub-001_ses-06_acq-rest_dir-AP_epi.nii.gz sub-001/ses-06/fmap/sub-001_ses-06_acq-rest_dir-PA_epi.nii.gz sub-001/ses-06/func sub-001/ses-06/func/sub-001_ses-06_task-rest_bold.nii.gz sub-001/ses-06/func/sub-001_ses-06_task-rest_bold.json sub-001/ses-06/func/sub-001_ses-06_task-hariri_bold.nii.gz sub-001/ses-06/func/sub-001_ses-06_task-hariri_bold.json sub-001/ses-06/func/sub-001_ses-06_task-hariri_events.tsv sub-001/ses-06/sub-001_ses-06_scans.json sub-001/ses-06/sub-001_ses-06_scans.tsv

fpichardo-umn commented 1 year ago

I removed the hariri files and copied the other files to a different space with fewer permissions issues. The pipeline finished without issue on several participatns.