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nipreps / mriqc

Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
http://mriqc.readthedocs.io
Apache License 2.0
299 stars 132 forks source link

MRIQC failing during IQM computation stage #1142

Closed tjhendrickson closed 7 months ago

tjhendrickson commented 1 year ago

What happened?

I'm attempting to run MRIQC on a large batch of images (~1,800). A majority complete without issue but several fail during the IQM computation stage. The inputted data between the successful and unsuccessful runs do not appear to be any different.

What command did you use?

/home/midb-ig/shared/HBCD/singularity_images/mriqc_23.1.0.sif \
/bids_dir /output_dir participant \
--participant_label ${subj_id} \
--session-id ${session_id} \
--work-dir /work \
--nprocs 5 \
--mem_gb 75 \
--no-sub \
-v

What version of the software are you running?

23.1.0

How are you running this software?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

Standard output logs:
230912-18:34:21,443 cli IMPORTANT:

    Running MRIQC version 23.1.0:
      * BIDS dataset path: /bids_dir.
      * Output folder: /output_dir.
      * Analysis levels: ['participant'].

230912-18:34:21,556 nipype.workflow INFO:
     Building anatomical MRIQC workflow (</bids_dir/sub-MOD1799/ses-V1a/anat/sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz>)..
230912-18:34:44,692 nipype.workflow INFO:
     Workflow mriqc_wf settings: ['check', 'execution', 'logging', 'monitoring']
230912-18:35:04,419 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.datalad_get".
230912-18:35:04,433 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.datalad_get" in "/work/mriqc_wf/anatMRIQC/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/datalad_get".
230912-18:35:04,434 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.datalad_get".
230912-18:35:04,471 nipype.workflow INFO:
     [Node] Executing "datalad_get" <mriqc.interfaces.datalad.DataladIdentityInterface>
230912-18:35:04,490 nipype.interface INFO:
     Datalad interface without dataset path defined.
230912-18:35:04,491 nipype.workflow INFO:
     [Node] Finished "datalad_get", elapsed time 0.000525s.
230912-18:35:06,449 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.conform".
230912-18:35:06,451 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.conform" in "/work/mriqc_wf/anatMRIQC/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/conform".
230912-18:35:06,451 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.conform".
230912-18:35:06,453 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.ComputeIQMs.metadata".
230912-18:35:06,463 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.ComputeIQMs.metadata" in "/work/mriqc_wf/anatMRIQC/ComputeIQMs/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/metadata".
230912-18:35:06,464 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.ComputeIQMs.metadata".
230912-18:35:06,493 nipype.workflow INFO:
     [Node] Executing "conform" <mriqc.interfaces.common.conform_image.ConformImage>
230912-18:35:06,501 nipype.workflow INFO:
     [Node] Executing "metadata" <niworkflows.interfaces.bids.ReadSidecarJSON>
230912-18:35:14,177 nipype.workflow INFO:
     [Node] Finished "conform", elapsed time 7.659132s.
230912-18:35:14,256 nipype.workflow INFO:
     [Node] Finished "metadata", elapsed time 7.739875s.
230912-18:35:14,418 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.synthstrip_wf.pre_clip".
230912-18:35:14,419 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.synthstrip_wf.pre_clip" in "/work/mriqc_wf/anatMRIQC/synthstrip_wf/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/pre_clip".
230912-18:35:14,420 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.synthstrip_wf.pre_clip".
230912-18:35:14,422 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.AirMaskWorkflow.RotationMask".
230912-18:35:14,423 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.AirMaskWorkflow.RotationMask" in "/work/mriqc_wf/anatMRIQC/AirMaskWorkflow/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/RotationMask".
230912-18:35:14,424 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.AirMaskWorkflow.RotationMask".
230912-18:35:14,426 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.anat_report_wf.PlotMosaicNoise".
230912-18:35:14,436 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.anat_report_wf.PlotMosaicNoise" in "/work/mriqc_wf/anatMRIQC/anat_report_wf/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/PlotMosaicNoise".
230912-18:35:14,436 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.anat_report_wf.PlotMosaicNoise".
230912-18:35:14,467 nipype.workflow INFO:
     [Node] Executing "pre_clip" <niworkflows.interfaces.nibabel.IntensityClip>
230912-18:35:14,473 nipype.workflow INFO:
     [Node] Executing "RotationMask" <mriqc.interfaces.anatomical.RotationMask>
230912-18:35:14,493 nipype.workflow INFO:
     [Node] Executing "PlotMosaicNoise" <nireports.interfaces.mosaic.PlotMosaic>
230912-18:35:16,261 nipype.workflow INFO:
     [Node] Finished "RotationMask", elapsed time 1.784387s.
230912-18:35:24,784 nipype.workflow INFO:
     [Node] Finished "PlotMosaicNoise", elapsed time 10.261003s.
230912-18:35:26,448 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.anat_report_wf.ds_report_background".
230912-18:35:26,448 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.anat_report_wf.ds_report_background" in "/work/mriqc_wf/anatMRIQC/anat_report_wf/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/ds_report_background".
230912-18:35:26,448 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.anat_report_wf.ds_report_background".
230912-18:35:26,500 nipype.workflow INFO:
     [Node] Executing "ds_report_background" <mriqc.interfaces.DerivativesDataSink>
230912-18:35:26,537 nipype.workflow INFO:
     [Node] Finished "ds_report_background", elapsed time 0.017623s.
230912-18:35:52,745 nipype.workflow INFO:
     [Node] Finished "pre_clip", elapsed time 38.275353s.
230912-18:35:54,488 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.synthstrip_wf.pre_n4".
230912-18:35:54,490 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.synthstrip_wf.pre_n4" in "/work/mriqc_wf/anatMRIQC/synthstrip_wf/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/pre_n4".
230912-18:35:54,491 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.synthstrip_wf.pre_n4".
230912-18:35:54,530 nipype.workflow INFO:
     [Node] Executing "pre_n4" <nipype.interfaces.ants.segmentation.N4BiasFieldCorrection>
230912-18:38:08,535 nipype.workflow INFO:
     [Node] Finished "pre_n4", elapsed time 133.752262s.
230912-18:38:10,667 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.synthstrip_wf.synthstrip".
230912-18:38:10,670 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.synthstrip_wf.synthstrip" in "/work/mriqc_wf/anatMRIQC/synthstrip_wf/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/synthstrip".
230912-18:38:10,671 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.synthstrip_wf.synthstrip".
230912-18:38:10,734 nipype.workflow INFO:
     [Node] Executing "synthstrip" <mriqc.interfaces.synthstrip.SynthStrip>
230912-18:39:49,452 nipype.workflow INFO:
     [Node] Finished "synthstrip", elapsed time 98.714853s.
230912-18:39:50,724 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.synthstrip_wf.post_n4".
230912-18:39:50,727 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.synthstrip_wf.post_n4" in "/work/mriqc_wf/anatMRIQC/synthstrip_wf/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/post_n4".
230912-18:39:50,727 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.synthstrip_wf.post_n4".
230912-18:39:50,729 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.ComputeIQMs.smoothness".
230912-18:39:50,731 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.ComputeIQMs.smoothness" in "/work/mriqc_wf/anatMRIQC/ComputeIQMs/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/smoothness".
230912-18:39:50,731 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.ComputeIQMs.smoothness".
230912-18:39:50,733 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.anat_report_wf.PlotMosaicZoomed".
230912-18:39:50,735 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.anat_report_wf.PlotMosaicZoomed" in "/work/mriqc_wf/anatMRIQC/anat_report_wf/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/PlotMosaicZoomed".
230912-18:39:50,735 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.anat_report_wf.PlotMosaicZoomed".
230912-18:39:50,767 nipype.workflow INFO:
     [Node] Executing "post_n4" <nipype.interfaces.ants.segmentation.N4BiasFieldCorrection>
230912-18:39:50,771 nipype.workflow INFO:
     [Node] Executing "smoothness" <nipype.interfaces.afni.utils.FWHMx>
230912-18:39:50,821 nipype.workflow INFO:
     [Node] Executing "PlotMosaicZoomed" <nireports.interfaces.mosaic.PlotMosaic>
230912-18:39:54,843 nipype.workflow INFO:
     [Node] Finished "smoothness", elapsed time 4.070691s.
230912-18:39:57,617 nipype.workflow INFO:
     [Node] Finished "PlotMosaicZoomed", elapsed time 6.792853s.
230912-18:39:58,698 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.anat_report_wf.ds_report_zoomed".
230912-18:39:58,699 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.anat_report_wf.ds_report_zoomed" in "/work/mriqc_wf/anatMRIQC/anat_report_wf/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/ds_report_zoomed".
230912-18:39:58,699 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.anat_report_wf.ds_report_zoomed".
230912-18:39:58,753 nipype.workflow INFO:
     [Node] Executing "ds_report_zoomed" <mriqc.interfaces.DerivativesDataSink>
230912-18:39:58,771 nipype.workflow INFO:
     [Node] Finished "ds_report_zoomed", elapsed time 0.015445s.
230912-18:40:17,209 nipype.workflow INFO:
     [Node] Finished "post_n4", elapsed time 26.195136s.
230912-18:40:18,735 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.synthstrip_wf.final_inu".
230912-18:40:18,736 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.synthstrip_wf.final_inu" in "/work/mriqc_wf/anatMRIQC/synthstrip_wf/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/final_inu".
230912-18:40:18,736 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.synthstrip_wf.final_inu".
230912-18:40:18,739 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.synthstrip_wf.final_masked".
230912-18:40:18,740 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.synthstrip_wf.final_masked" in "/work/mriqc_wf/anatMRIQC/synthstrip_wf/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/final_masked".
230912-18:40:18,740 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.synthstrip_wf.final_masked".
230912-18:40:18,743 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.SpatialNormalization.SpatialNormalization".
230912-18:40:18,744 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.SpatialNormalization.SpatialNormalization" in "/work/mriqc_wf/anatMRIQC/SpatialNormalization/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/SpatialNormalization".
230912-18:40:18,745 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.SpatialNormalization.SpatialNormalization".
230912-18:40:18,780 nipype.workflow INFO:
     [Node] Executing "final_masked" <niworkflows.interfaces.nibabel.ApplyMask>
230912-18:40:18,789 nipype.workflow INFO:
     [Node] Executing "SpatialNormalization" <niworkflows.interfaces.reportlets.registration.SpatialNormalizationRPT>
230912-18:40:18,834 nipype.workflow INFO:
     [Node] Executing "final_inu" <nipype.interfaces.utility.wrappers.Function>
230912-18:40:20,566 nipype.workflow INFO:
     [Node] Finished "final_masked", elapsed time 1.7831519999999998s.
230912-18:40:21,322 nipype.workflow INFO:
     [Node] Finished "final_inu", elapsed time 2.485094s.
230912-18:42:19,774 nipype.workflow INFO:
     [Node] Finished "SpatialNormalization", elapsed time 120.982838s.
230912-18:42:22,844 nipype.workflow INFO:
     [Node] Outdated cache found for "_tpms_std2t1w0".
230912-18:42:22,847 nipype.workflow INFO:
     [Node] Setting-up "_tpms_std2t1w0" in "/work/mriqc_wf/anatMRIQC/SpatialNormalization/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/tpms_std2t1w/mapflow/_tpms_std2t1w0".
230912-18:42:22,847 nipype.workflow INFO:
     [Node] Outdated cache found for "_tpms_std2t1w0".
230912-18:42:22,848 nipype.workflow INFO:
     [Node] Outdated cache found for "_tpms_std2t1w1".
230912-18:42:22,850 nipype.workflow INFO:
     [Node] Setting-up "_tpms_std2t1w1" in "/work/mriqc_wf/anatMRIQC/SpatialNormalization/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/tpms_std2t1w/mapflow/_tpms_std2t1w1".
230912-18:42:22,850 nipype.workflow INFO:
     [Node] Outdated cache found for "_tpms_std2t1w1".
230912-18:42:22,852 nipype.workflow INFO:
     [Node] Outdated cache found for "_tpms_std2t1w2".
230912-18:42:22,853 nipype.workflow INFO:
     [Node] Setting-up "_tpms_std2t1w2" in "/work/mriqc_wf/anatMRIQC/SpatialNormalization/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/tpms_std2t1w/mapflow/_tpms_std2t1w2".
230912-18:42:22,854 nipype.workflow INFO:
     [Node] Outdated cache found for "_tpms_std2t1w2".
230912-18:42:22,886 nipype.workflow INFO:
     [Node] Executing "_tpms_std2t1w0" <niworkflows.interfaces.fixes.FixHeaderApplyTransforms>
230912-18:42:22,901 nipype.workflow INFO:
     [Node] Executing "_tpms_std2t1w2" <niworkflows.interfaces.fixes.FixHeaderApplyTransforms>
230912-18:42:22,926 nipype.workflow INFO:
     [Node] Executing "_tpms_std2t1w1" <niworkflows.interfaces.fixes.FixHeaderApplyTransforms>
230912-18:42:27,82 nipype.workflow INFO:
     [Node] Finished "_tpms_std2t1w2", elapsed time 4.1787469999999995s.
230912-18:42:27,701 nipype.workflow INFO:
     [Node] Finished "_tpms_std2t1w1", elapsed time 4.772178s.
230912-18:42:28,325 nipype.workflow INFO:
     [Node] Finished "_tpms_std2t1w0", elapsed time 4.34536s.
230912-18:42:28,850 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.SpatialNormalization.tpms_std2t1w".
230912-18:42:28,854 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.SpatialNormalization.tpms_std2t1w".
230912-18:42:28,888 nipype.workflow INFO:
     [Node] Setting-up "_tpms_std2t1w0" in "/work/mriqc_wf/anatMRIQC/SpatialNormalization/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/tpms_std2t1w/mapflow/_tpms_std2t1w0".
230912-18:42:28,890 nipype.workflow INFO:
     [Node] Cached "_tpms_std2t1w0" - collecting precomputed outputs
230912-18:42:28,890 nipype.workflow INFO:
     [Node] "_tpms_std2t1w0" found cached.
230912-18:42:28,891 nipype.workflow INFO:
     [Node] Setting-up "_tpms_std2t1w1" in "/work/mriqc_wf/anatMRIQC/SpatialNormalization/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/tpms_std2t1w/mapflow/_tpms_std2t1w1".
230912-18:42:28,892 nipype.workflow INFO:
     [Node] Cached "_tpms_std2t1w1" - collecting precomputed outputs
230912-18:42:28,892 nipype.workflow INFO:
     [Node] "_tpms_std2t1w1" found cached.
230912-18:42:28,893 nipype.workflow INFO:
     [Node] Setting-up "_tpms_std2t1w2" in "/work/mriqc_wf/anatMRIQC/SpatialNormalization/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/tpms_std2t1w/mapflow/_tpms_std2t1w2".
230912-18:42:28,895 nipype.workflow INFO:
     [Node] Cached "_tpms_std2t1w2" - collecting precomputed outputs
230912-18:42:28,895 nipype.workflow INFO:
     [Node] "_tpms_std2t1w2" found cached.
230912-18:42:30,860 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.HeadMaskWorkflow.Enhance".
230912-18:42:30,862 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.HeadMaskWorkflow.Enhance" in "/work/mriqc_wf/anatMRIQC/HeadMaskWorkflow/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/Enhance".
230912-18:42:30,862 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.HeadMaskWorkflow.Enhance".
230912-18:42:30,863 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.brain_tissue_segmentation.format_tpm_names".
230912-18:42:30,865 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.brain_tissue_segmentation.format_tpm_names" in "/work/mriqc_wf/anatMRIQC/brain_tissue_segmentation/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/format_tpm_names".
230912-18:42:30,865 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.brain_tissue_segmentation.format_tpm_names".
230912-18:42:30,905 nipype.workflow INFO:
     [Node] Executing "Enhance" <nipype.interfaces.utility.wrappers.Function>
230912-18:42:30,935 nipype.workflow INFO:
     [Node] Executing "format_tpm_names" <nipype.interfaces.utility.wrappers.Function>
230912-18:42:33,702 nipype.workflow INFO:
     [Node] Finished "Enhance", elapsed time 2.7943670000000003s.
230912-18:42:34,200 nipype.workflow INFO:
     [Node] Finished "format_tpm_names", elapsed time 3.262911s.
230912-18:42:34,893 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.HeadMaskWorkflow.Grad".
230912-18:42:34,894 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.HeadMaskWorkflow.Grad" in "/work/mriqc_wf/anatMRIQC/HeadMaskWorkflow/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/Grad".
230912-18:42:34,895 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.HeadMaskWorkflow.Grad".
230912-18:42:34,898 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.HeadMaskWorkflow.apply_mask".
230912-18:42:34,899 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.HeadMaskWorkflow.apply_mask" in "/work/mriqc_wf/anatMRIQC/HeadMaskWorkflow/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/apply_mask".
230912-18:42:34,900 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.HeadMaskWorkflow.apply_mask".
230912-18:42:34,953 nipype.workflow INFO:
     [Node] Executing "Grad" <nipype.interfaces.utility.wrappers.Function>
230912-18:42:34,973 nipype.workflow INFO:
     [Node] Executing "apply_mask" <niworkflows.interfaces.nibabel.ApplyMask>
230912-18:42:36,249 nipype.workflow INFO:
     [Node] Finished "apply_mask", elapsed time 1.273661s.
230912-18:42:36,886 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.brain_tissue_segmentation.segmentation".
230912-18:42:36,889 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.brain_tissue_segmentation.segmentation" in "/work/mriqc_wf/anatMRIQC/brain_tissue_segmentation/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/segmentation".
230912-18:42:36,889 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.brain_tissue_segmentation.segmentation".
230912-18:42:36,956 nipype.workflow INFO:
     [Node] Executing "segmentation" <nipype.interfaces.ants.segmentation.Atropos>
230912-18:42:39,808 nipype.workflow INFO:
     [Node] Finished "Grad", elapsed time 4.852234s.
230912-18:42:40,913 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.HeadMaskWorkflow.GradientThreshold".
230912-18:42:40,914 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.HeadMaskWorkflow.GradientThreshold" in "/work/mriqc_wf/anatMRIQC/HeadMaskWorkflow/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/GradientThreshold".
230912-18:42:40,915 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.HeadMaskWorkflow.GradientThreshold".
230912-18:42:41,37 nipype.workflow INFO:
     [Node] Executing "GradientThreshold" <nipype.interfaces.utility.wrappers.Function>
230912-18:43:12,216 nipype.workflow INFO:
     [Node] Finished "GradientThreshold", elapsed time 31.176172s.
230912-18:43:12,873 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.AirMaskWorkflow.ArtifactMask".
230912-18:43:12,874 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.AirMaskWorkflow.ArtifactMask" in "/work/mriqc_wf/anatMRIQC/AirMaskWorkflow/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/ArtifactMask".
230912-18:43:12,875 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.AirMaskWorkflow.ArtifactMask".
230912-18:43:12,915 nipype.workflow INFO:
     [Node] Executing "ArtifactMask" <mriqc.interfaces.anatomical.ArtifactMask>
230912-18:43:18,725 nipype.workflow INFO:
     [Node] Finished "ArtifactMask", elapsed time 5.80849s.
230912-18:43:20,962 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.ComputeIQMs.provenance".
230912-18:43:20,963 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.ComputeIQMs.provenance" in "/work/mriqc_wf/anatMRIQC/ComputeIQMs/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/provenance".
230912-18:43:20,963 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.ComputeIQMs.provenance".
230912-18:43:21,12 nipype.workflow INFO:
     [Node] Executing "provenance" <mriqc.interfaces.reports.AddProvenance>
230912-18:43:21,198 nipype.workflow INFO:
     [Node] Finished "provenance", elapsed time 0.184381s.
230912-18:43:21,340 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.ComputeIQMs.ComputeQI2".
230912-18:43:21,342 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.ComputeIQMs.ComputeQI2" in "/work/mriqc_wf/anatMRIQC/ComputeIQMs/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/ComputeQI2".
230912-18:43:21,342 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.ComputeIQMs.ComputeQI2".
230912-18:43:21,391 nipype.workflow INFO:
     [Node] Executing "ComputeQI2" <mriqc.interfaces.anatomical.ComputeQI2>
230912-18:43:34,914 nipype.workflow INFO:
     [Node] Finished "ComputeQI2", elapsed time 13.520793s.
230912-18:43:52,723 nipype.workflow INFO:
     [Node] Finished "segmentation", elapsed time 75.740508s.
230912-18:43:52,936 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.ComputeIQMs.harmonize".
230912-18:43:52,938 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.ComputeIQMs.harmonize" in "/work/mriqc_wf/anatMRIQC/ComputeIQMs/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/harmonize".
230912-18:43:52,938 nipype.workflow INFO:
     [Node] Outdated cache found for "mriqc_wf.anatMRIQC.ComputeIQMs.harmonize".
230912-18:43:52,997 nipype.workflow INFO:
     [Node] Executing "harmonize" <mriqc.interfaces.anatomical.Harmonize>
230912-18:43:54,486 nipype.workflow INFO:
     [Node] Finished "harmonize", elapsed time 1.48734s.
230912-18:43:54,920 nipype.workflow INFO:
     [Node] Setting-up "mriqc_wf.anatMRIQC.ComputeIQMs.measures" in "/work/mriqc_wf/anatMRIQC/ComputeIQMs/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/measures".
230912-18:43:54,989 nipype.workflow INFO:
     [Node] Executing "measures" <mriqc.interfaces.anatomical.StructuralQC>
230912-18:43:55,463 nipype.workflow INFO:
     [Node] Finished "measures", elapsed time 0.418996s.
230912-18:43:55,463 nipype.workflow WARNING:
     Storing result file without outputs
230912-18:43:55,473 nipype.workflow WARNING:
     [Node] Error on "mriqc_wf.anatMRIQC.ComputeIQMs.measures" (/work/mriqc_wf/anatMRIQC/ComputeIQMs/_in_file_..bids_dir..sub-MOD1799..ses-V1a..anat..sub-MOD1799_ses-V1a_acq-MPR_run-01_space-individual_den-BCP_T1w.nii.gz/measures)
230912-18:43:56,810 nipype.workflow ERROR:
     Node measures.a0 failed to run on host acl39.
230912-18:43:56,810 nipype.workflow ERROR:
     Saving crash info to /output_dir/logs/crash-20230912-184356-hendr522-measures.a0-ba474740-ecfe-4731-be8c-1f79c8218eda.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.9/site-packages/mriqc/engine/plugin.py", line 60, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node measures.

Traceback:
    Traceback (most recent call last):
      File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 397, in run
        runtime = self._run_interface(runtime)
      File "/opt/conda/lib/python3.9/site-packages/mriqc/interfaces/anatomical.py", line 114, in _run_interface
        raise RuntimeError(
    RuntimeError: Input inhomogeneity-corrected data seem empty. MRIQC failed to process this dataset.

Standard error logs:
Traceback (most recent call last):
  File "/opt/conda/bin/mriqc", line 8, in <module>
    sys.exit(main())
  File "/opt/conda/lib/python3.9/site-packages/mriqc/cli/run.py", line 168, in main
    mriqc_wf.run(**_plugin)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/opt/conda/lib/python3.9/site-packages/mriqc/engine/plugin.py", line 184, in run
    self._clean_queue(jobid, graph, result=result)
  File "/opt/conda/lib/python3.9/site-packages/mriqc/engine/plugin.py", line 256, in _clean_queue
    raise RuntimeError("".join(result["traceback"]))
RuntimeError: Traceback (most recent call last):
  File "/opt/conda/lib/python3.9/site-packages/mriqc/engine/plugin.py", line 60, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node measures.

Traceback:
    Traceback (most recent call last):
      File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 397, in run
        runtime = self._run_interface(runtime)
      File "/opt/conda/lib/python3.9/site-packages/mriqc/interfaces/anatomical.py", line 114, in _run_interface
        raise RuntimeError(
    RuntimeError: Input inhomogeneity-corrected data seem empty. MRIQC failed to process this dataset.

Additional information / screenshots

No response

tjhendrickson commented 1 year ago

Any update on this? @oesteban

oesteban commented 8 months ago

@tjhendrickson did you manage to figure out? I am allocating some bandwidth to mriqc these days.

oesteban commented 7 months ago

@tjhendrickson I have checked and there might be a problem with the N4BiasFieldCorrection node. Would you be able to provide an example dataset of this?

cc/ @smeisler since he thumbed-up the issue.

tjhendrickson commented 7 months ago

Hi @oesteban, I haven't had a chance to return back to this of recent. I'll make a note to test it out again and should be able to include an example dataset if I am still running into issues.

Best,

-Tim

tjhendrickson commented 7 months ago

Hi @oesteban, I looked into this again and found a dataset that failed that I can share with you. How should I share the dataset with you? If you would prefer, feel free to reach out to me directly via e-mail at hendr522@umn.edu.

-Tim

oesteban commented 7 months ago

As per our discussion over email (thanks @tjhendrickson for letting me eyeball one of the failing cases), the problem is that MRIQC doesn't work on infant images for the time being.

cc/ @mgxd to tap on the interest for adaptions for babies :)