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Error when running on fmri timeseries #1416

@gbook

Description

@gbook

I've had success with running mriqc on T1 images, but I have not been able to get it to work on fmri timeseries. What might be going wrong?

The input /data directory contains:

data
├── README
├── dataset_description.json
├── participants.tsv
└── sub-S1234ABC
    └── ses-70
        └── func
            ├── sub-S1234ABC_ses-70_bold.json
            └── sub-S1234ABC_ses-70_bold.nii.gz

The error I get is

[nidb@ado2 bin]$ /nidb/qcmodules/mriqc/./mriqc.sh /nidb/data/archive/S1234ABC/70/6/qc/mriqc_docker/data /nidb/data/archive/S1234ABC/70/6/qc/mriqc_docker/output S1234ABC
Emulate Docker CLI using podman. Create /etc/containers/nodocker to quiet msg.
------------------------------------------------------------------
  Running MRIQC version 25.1.0.dev45+g699d1691
  ----------------------------------------------------------------

  NOTICE
  Copyright © The NiPreps Developers.

  This product includes software developed by
  the NiPreps Community (https://nipreps.org/).

  Portions of this software were developed at the Department of
  Psychology at Stanford University, Stanford, CA, US.

  This software contains code ultimately derived from the
  PCP Quality Assessment Protocol (QAP;
  http://preprocessed-connectomes-project.org/quality-assessment-protocol)
  by C. Craddock, S. Giavasis, D. Clark, Z. Shezhad, and J. Pellman.

  This software is also distributed as a Docker container image.
  The bootstrapping file for the image ("Dockerfile") is licensed
  under the MIT License.

  ----------------------------------------------------------------

  * BIDS dataset path: /data.
  * Output folder: /out.
  * Analysis levels: ['participant'].
------------------------------------------------------------------

2025-09-10 14:55:18 | IMPORTANT | mriqc            | Extracting metadata and entities for 1 input runs of modality 'bold'...
2025-09-10 14:55:18 | IMPORTANT | mriqc            | File size ('bold'): 0.04|0.04 GB [maximum|average].
2025-09-10 14:55:22 | IMPORTANT | mriqc            | Building MRIQC's workflows...
2025-09-10 14:55:28 | IMPORTANT | mriqc            | Workflow building finished (exit code 0).
2025-09-10 14:57:43 | WARNING  | nipype.workflow  | Storing result file without outputs
2025-09-10 14:57:43 | WARNING  | nipype.workflow  | [Node] Error on "_ds_report_mean0" (/tmp/work/mriqc_wf/funcMRIQC/func_report_wf/bf5caffaa7ac8be6164915dd928dd5093f153e61/ds_report_mean/mapflow/_ds_report_mean0)
2025-09-10 14:57:43 | WARNING  | nipype.workflow  | Storing result file without outputs
2025-09-10 14:57:43 | WARNING  | nipype.workflow  | [Node] Error on "mriqc_wf.funcMRIQC.func_report_wf.ds_report_mean" (/tmp/work/mriqc_wf/funcMRIQC/func_report_wf/bf5caffaa7ac8be6164915dd928dd5093f153e61/ds_report_mean)
Traceback (most recent call last):
  File "/opt/conda/lib/python3.11/site-packages/mriqc/engine/plugin.py", line 579, in _send_procs_to_workers
    self.procs[jobid].run(updatehash=updatehash)
  File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 1380, in _run_interface
    result = self._collate_results(
             ^^^^^^^^^^^^^^^^^^^^^^

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