Summary of what happened
Hello everyone,
I’m running fmriprep (v24.1.1) on an HCP cluster in a dataset with ~350 participants. From these, only 23 participants finished successfully, and the rest finished the fmriprep process but had an error when creating the reports. I am trying to run fmriprep with the `–reports-only` flag, and it still fails. In both cases, the last line of the error points towards a different participant.
Do you have any idea of what might be creating the problem and how to fix it?
Thank you
Command used (and if a helper script was used, a link to the helper script or the command generated)
- For the first run
export APPTAINERENV_TEMPLATEFLOW_HOME=${proj_path}/templateflow
export APPTAINER_BINDPATH=$APPTAINERENV_TEMPLATEFLOW_HOME
export APPTAINER_BIND=${proj_path},${input},${output_fmriprep},${output_fmriprep}/logs,$APPTAINERENV_TEMPLATEFLOW_HOME
singularity run --cleanenv -B ${proj_path}:/scratch -B $APPTAINERENV_TEMPLATEFLOW_HOME ${proj_path}/fmriprep-24.1.1.simg \
${input} ${output_fmriprep} participant \
--participant-label ${SUBJECT} \
--skip_bids_validation \
--nthreads 16 \
--omp-nthreads 16 \
--low-mem \
--longitudinal \
--output-spaces anat MNI152NLin2009cAsym:res-2 \
--fs-license-file ${proj_path}/fs_license.txt \
--fs-no-reconall \
--output-layout bids \
--work-dir ${output_fmriprep}
- For
--reports only
export APPTAINERENV_TEMPLATEFLOW_HOME=${proj_path}/templateflow
export APPTAINER_BINDPATH=$APPTAINERENV_TEMPLATEFLOW_HOME
export APPTAINER_BIND=${proj_path},${input},${output_fmriprep},${output_fmriprep}/logs,$APPTAINERENV_TEMPLATEFLOW_HOME
singularity run --cleanenv -B ${proj_path}:/scratch -B $APPTAINERENV_TEMPLATEFLOW_HOME ${proj_path}/fmriprep-24.1.1.simg \
${input} ${output_fmriprep} participant \
--participant-label ${SUBJECT} \
--skip_bids_validation \
--reports-only \
--fs-license-file ${proj_path}/fs_license.txt \
--work-dir ${output_fmriprep}
Version
24.1.1
Environment (Docker, Singularity, custom installation)
Docker in HCP
BIDS Validity (could generally say “Are your data formatted according to a validatable standard? Please provide the output of the validator.”)
Data is validated
Relevant log outputs (maybe prompt for 20 lines)
- For the first run (Running for participant sub-06VPJN)
260309-20:13:56,605 nipype.workflow INFO:
[Node] Finished "ds_bold", elapsed time 91.114476s.
2026-03-09 20:13:56,605 [ INFO] [Node] Finished "ds_bold", elapsed time 91.114476s.
260309-20:13:59,742 nipype.workflow IMPORTANT:
fMRIPrep finished successfully!
2026-03-09 20:13:59,742 [IMPORTANT] fMRIPrep finished successfully!
260309-20:13:59,749 nipype.workflow IMPORTANT:
Works derived from this fMRIPrep execution should include the boilerplate text found in <OUTPUT_PATH>/logs/CITATION.md.
2026-03-09 20:13:59,749 [IMPORTANT] Works derived from this fMRIPrep execution should include the boilerplate text found in <OUTPUT_PATH>/logs/CITATION.md.
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/bin/fmriprep", line 8, in <module>
sys.exit(main())
^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/cli/run.py", line 228, in main
failed_reports = generate_reports(
^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/reports/core.py", line 100, in generate_reports
report_error = run_reports(
^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/reports/core.py", line 43, in run_reports
robj = Report(
^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nireports/assembler/report.py", line 327, in __init__
self.index(settings)
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nireports/assembler/report.py", line 350, in index
layout = BIDSLayout(
^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/bids/layout/layout.py", line 177, in __init__
_indexer(self)
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/bids/layout/index.py", line 148, in __call__
all_bfs, all_tag_dicts = self._index_dir(self._layout._root, self._config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/bids/layout/index.py", line 239, in _index_dir
dir_bfs, dir_tag_dicts = self._index_dir(d, config, force=force)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/bids/layout/index.py", line 208, in _index_dir
_, dirnames, filenames = next(path.fs.walk(path.path))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
StopIteration: ('<path_to_output_folder>/fmriprep/sub-1PPFYF', [], [])
- For
--reports-only(Running for participant sub-06VPJN)
2026-03-20 15:55:37,865 [IMPORTANT] Running fMRIPrep version 24.1.1
License NOTICE ##################################################
fMRIPrep 24.1.1
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 is also distributed as a Docker container image.
The bootstrapping file for the image ("Dockerfile") is licensed
under the MIT License.
This software may be distributed through an add-on package called
"Docker Wrapper" that is under the BSD 3-clause License.
#################################################################
260320-15:55:38,9 nipype.workflow IMPORTANT:
Running --reports-only on participants 06VPJN
2026-03-20 15:55:38,009 [IMPORTANT] Running --reports-only on participants 06VPJN
Process Process-2:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.11/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/opt/conda/envs/fmriprep/lib/python3.11/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/cli/workflow.py", line 94, in build_workflow
failed_reports = generate_reports(
^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/reports/core.py", line 100, in generate_reports
report_error = run_reports(
^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/reports/core.py", line 43, in run_reports
robj = Report(
^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nireports/assembler/report.py", line 327, in __init__
self.index(settings)
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nireports/assembler/report.py", line 350, in index
layout = BIDSLayout(
^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/bids/layout/layout.py", line 177, in __init__
_indexer(self)
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/bids/layout/index.py", line 148, in __call__
all_bfs, all_tag_dicts = self._index_dir(self._layout._root, self._config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/bids/layout/index.py", line 239, in _index_dir
dir_bfs, dir_tag_dicts = self._index_dir(d, config, force=force)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/bids/layout/index.py", line 208, in _index_dir
_, dirnames, filenames = next(path.fs.walk(path.path))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
StopIteration: ('<path_to_output_folder>/fmriprep/sub-SXGP7U', [], [])