Hi all - long time listener, first time caller. I’m having problems running qsiprep - please see below for details.
Many thanks!
Oli
Summary of what happened:
Attempting to run qsiprep using T1w and dwi data was inputs. Completes fine in some subjects/sessions, but some encounter a fatal error. I can’t tell why some do and some do not complete, but hoping that this will help me figure that out.
Command used (and if a helper script was used, a link to the helper script or the command generated):
parallel --verbose --progress -j 2 \
docker run --gpus all --rm \
-e DOCKER_VERSION_8395080871=29.1.3 \
--mount type=bind,source=$HOMEDIR,dst=$HOMEDIR \
-v /home/hackerman/Desktop/ssd_workdir:/home/hackerman/Desktop/ssd_workdir:rw \
-v ${HOMEDIR}/bids_complete:${HOMEDIR}/bids_complete:ro \
-v ${HOMEDIR}/derivatives:${HOMEDIR}/derivatives:rw \
-v $FSLICK:/opt/freesurfer/license.txt:ro \
pennlinc/qsiprep:26.1.0 \
$HOMEDIR/bids_complete \
${HOMEDIR}/derivatives/qsiprep \
-w /home/hackerman/Desktop/ssd_workdir/temp_{} \
--output-resolution 2 \
participant \
--verbose \
--sdc-anat-reference synb0 \
--gpu {diffprep,drbuddi,eddy} \
--subject-anatomical-reference sessionwise \
--anat-modality T1w \
--participant-label {} \
--skip-bids-validation ::: $subs
CODE HERE
Version:
qsiprep version = “26.1.0”
Environment (Docker, Singularity / Apptainer, custom installation):
docker DOCKER_VERSION_8395080871=29.1.3
Data formatted according to a validatable standard? Please provide the output of the validator:
Converted using dcm2bids but I skip bids validation
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
<!-- Below thisTraceback (most recent call last):
File "/app/.pixi/envs/qsiprep/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/qsiprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 546, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/qsiprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 661, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/qsiprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 787, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node mask_template.
Cmdline:
3dcalc -a /home/hackerman/Desktop/ssd_workdir/temp_sub-3124/qsiprep_26_1_wf/sub_3124_ses_20140528_wf/anat_preproc_wf/get_template_image/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz -b /home/hackerman/Desktop/ssd_workdir/temp_sub-3124/qsiprep_26_1_wf/sub_3124_ses_20140528_wf/anat_preproc_wf/get_template_image/tpl-MNI152NLin2009cAsym_res-01_desc-brain_mask.nii.gz -expr "a*b" -prefix tpl-MNI152NLin2009cAsym_res-01_T1w_calc.nii.gz
Stdout:
Stderr:
++ 3dcalc: AFNI version=AFNI_25.2.09 (Aug 24 2025) [64-bit]
++ Authored by: A cast of thousands
++ WARNING: nifti_read_buffer(/home/hackerman/Desktop/ssd_workdir/temp_sub-3124/qsiprep_26_1_wf/sub_3124_ses_20140528_wf/anat_preproc_wf/get_template_image/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz):
data bytes needed = 17060042
data bytes input = 12547649
number missing = 4512393 (set to 0)
** NIFTI load bricks: cannot read brick 0 from '/home/hackerman/Desktop/ssd_workdir/temp_sub-3124/qsiprep_26_1_wf/sub_3124_ses_20140528_wf/anat_preproc_wf/get_template_image/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz'
e[7m** FATAL ERROR:e[0m Can't load dataset '/home/hackerman/Desktop/ssd_workdir/temp_sub-3124/qsiprep_26_1_wf/sub_3124_ses_20140528_wf/anat_preproc_wf/get_template_image/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz': is it complete?
** Program compile date = Aug 24 2025 line, provide any other information that might be meaningful. This could be screenshots, troubleshooting steps you have tried, or information about your operating system, etc. -->