Summary of what happened:
Hi everyone,
I’m running fMRIPrep (v25.2.4) on one subject via Docker on macOS, however, I get an error in my .html. I would appreciate any help and indication on what is the problem and how it can be fixed.
Command used (and if a helper script was used, a link to the helper script or the command generated):
FMRIPREP_CMD="/Users/*/Library/Python/3.9/bin/fmriprep-docker"
if [ ! -f "$FMRIPREP_CMD" ]; then
echo "ERROR: fmriprep-docker not found at $FMRIPREP_CMD"
exit 1
fi
mem=${mem//[!0-9]/}
mem_mb=$(( (mem * 1000) - 5000 ))
export TEMPLATEFLOW_HOME=$HOME/.cache/templateflow
"$FMRIPREP_CMD" "$bids_root_dir" "$bids_root_dir/derivatives" \
participant \
--participant-label "$subj" \
--fs-license-file "$bids_root_dir/derivatives/license.txt" \
--output-spaces MNI152NLin2009cAsym:res-2 \
--nthreads "$nthreads" \
--mem_mb "$mem_mb" \
--stop-on-first-crash \
-w /tmp
Version:
25.2.4
Environment (Docker, Singularity / Apptainer, custom installation):
Docker
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
The resulting files/folder structure after running fmriprep is:
├── dataset_description.json
├── license.txt
├── logs
│ ├── CITATION.bib
│ ├── CITATION.html
│ ├── CITATION.md
│ └── CITATION.tex
├── sourcedata
│ └── freesurfer
│ └── fsaverage
│ ├── label
│ ├── mri
│ ├── mri.2mm
│ ├── scripts
│ ├── surf
│ └── xhemi
├── sub-1001
│ ├── figures
│ │ ├── sub-1001_desc-about_T1w.html
│ │ ├── sub-1001_desc-conform_T1w.html
│ │ ├── sub-1001_desc-summary_T1w.html
│ │ ├── sub-1001_task-AST_dir-PA_desc-validation_bold.html
│ │ ├── sub-1001_task-MT_dir-PA_desc-validation_bold.html
│ │ ├── sub-1001_task-Rest_dir-PA_desc-validation_bold.html
│ │ └── sub-1001_task-SST_dir-PA_desc-validation_bold.html
│ ├── func
│ │ ├── sub-1001_task-AST_dir-PA_desc-hmc_boldref.json
│ │ ├── sub-1001_task-AST_dir-PA_desc-hmc_boldref.nii.gz
│ │ ├── sub-1001_task-MT_dir-PA_desc-hmc_boldref.json
│ │ ├── sub-1001_task-MT_dir-PA_desc-hmc_boldref.nii.gz
│ │ ├── sub-1001_task-Rest_dir-PA_desc-hmc_boldref.json
│ │ ├── sub-1001_task-Rest_dir-PA_desc-hmc_boldref.nii.gz
│ │ ├── sub-1001_task-SST_dir-PA_desc-hmc_boldref.json
│ │ └── sub-1001_task-SST_dir-PA_desc-hmc_boldref.nii.gz
│ └── log
│ └── 20260304-122404_f04807d4-6b51-4d36-8161-a411caf89e6d
│ ├── crash-20260304-122622-root-slice_timing_correction-dba9af24-815f-4e1c-92a3-771ab7cfe3ec.txt
│ └── fmriprep.toml
└── sub-1001.html
As can be seen, there are no preprocessed anatomical data and quite frankly, I am not understanding much of this output data.
The subject .html shows:
Traceback (most recent call last):
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError:
Exception raised while executing Node slice_timing_correction.
Cmdline:
3dTshift \
-ignore 1 \
-prefix sub-1001_task-SST_dir-PA_bold_tshift.nii.gz \
-tpattern @slice_timing.1D \
-TR 1.5s \
-tzero 0.699 \
/scratch/fmriprep_25_2_wf/sub_1001_wf/bold_task_SST_dir_PA_wf/bold_native_wf/bold_stc_wf/slice_timing_correction/sub-1001_task-SST_dir-PA_bold.nii.gz
Stdout:
Stderr:
++ 3dTshift: AFNI version=AFNI_25.2.09 (Aug 24 2025) [64-bit]
** AFNI converts NIFTI_datatype=512 (UINT16) in file
/scratch/fmriprep_25_2_wf/sub_1001_wf/bold_task_SST_dir_PA_wf/bold_native_wf/bold_stc_wf/slice_timing_correction/sub-1001_task-SST_dir-PA_bold.nii.gz
to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
*+ WARNING:
If you are performing spatial transformations on an oblique dset, such as
/scratch/fmriprep_25_2_wf/sub_1001_wf/bold_task_SST_dir_PA_wf/bold_native_wf/bold_stc_wf/slice_timing_correction/sub-1001_task-SST_dir-PA_bold.nii.gz,
or viewing/combining it with volumes of differing obliquity, you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See `3dWarp -help` for details.
++ Oblique dataset:
/scratch/fmriprep_25_2_wf/sub_1001_wf/bold_task_SST_dir_PA_wf/bold_native_wf/bold_stc_wf/slice_timing_correction/sub-1001_task-SST_dir-PA_bold.nii.gz
is 18.275352 degrees from plumb.
Killed
Traceback:
RuntimeError: subprocess exited with code 137
Apologies for the long message but I am utterly confused about what happened and what I am looking at. I’ll appreciate any help!
Thanks in advance!!