QSIrecon throwing errors when calculating connectivity from pre-installed atlases and hanging

[samuelholly]

Summary

QSIrecon throwing errors when calculating connectivity from pre-installed atlases and hanging

Additional details

• QSIRecon version: 0.23.2
• Docker version: 4.10.1
• Singularity version: NA

What were you trying to do?

I tried to run the dsi_studio_gqi recon pipeline on my data preprocessed with qsiprep (v 0.19.1).

What did you expect to happen?

That the pipeline will complete succesfully.

What actually happened?

Started getting errors and even after a few hours, there was no progress.

Reproducing the bug

This is the command I ran from my Powershell:

docker run -ti --rm \
    -v H:\qsiprep_out\qsiprep:/data \
    -v H:\qsirecon_out:/out \
    -v W:\license.txt:/opt/freesurfer/license.txt \
    pennlinc/qsirecon:0.23.2 \
    /data /out participant \
    --fs-license-file /opt/freesurfer/license.txt \
    --output-resolution 2 \
    --recon-spec dsi_studio_gqi \
    -vv \
    --n_cpus 8 \
    --resource-monitor \
    --write-graph \
    --notrack \
    --participant-label 019

This is the output in my PS window:

...
241018-11:39:35,87 nipype.workflow WARNING:
         [Node] Error on "dsistudio_atlasgraph.aal116" (/tmp/work/qsirecon_0_23_wf/sub-019_dsistudio_pipeline/sub_019_acq_ep2ddtib3000tra64p2_dir_AP_space_T1w_desc_preproc_recon_wf/streamline_connectivity/calc_connectivity/dsistudio_atlasgraph/aal116)
241018-11:39:37,100 nipype.workflow ERROR:
         Node aal116 failed to run on host cacc95b69241.
241018-11:39:37,229 nipype.workflow ERROR:
         Saving crash info to /tmp/crash-20241018-113937-root-aal116-a5f74bb4-9c50-4fa7-8981-7c93f2772656.pklz
Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/qsiprep/lib/python3.10/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 aal116.

Cmdline:
        dsi_studio --action=ana  --connectivity=/tmp/work/qsirecon_0_23_wf/sub-019_dsistudio_pipeline/sub_019_acq_ep2ddtib3000tra64p2_dir_AP_space_T1w_desc_preproc_dwi_specific_anat_wf/get_atlases/tpl-MNI152NLin2009cAsym_res-01_atlas-AAL116_desc-LPS_dseg_to_dwi.nii.gz --connectivity_type=pass,end --connectivity_value=count,ncount,mean_length,gfa --source=/tmp/work/qsirecon_0_23_wf/sub-019_dsistudio_pipeline/sub_019_acq_ep2ddtib3000tra64p2_dir_AP_space_T1w_desc_preproc_recon_wf/streamline_connectivity/calc_connectivity/dsistudio_atlasgraph/aal116/sub-019_acq-ep2ddtib3000tra64p2_dir-AP_space-T1w_desc-preproc_dwi.src.gz.odf.gqi.1.25.fib.gz --thread_count=1 --thread_count=1 --tract=/tmp/work/qsirecon_0_23_wf/sub-019_dsistudio_pipeline/sub_019_acq_ep2ddtib3000tra64p2_dir_AP_space_T1w_desc_preproc_recon_wf/streamline_connectivity/calc_connectivity/dsistudio_atlasgraph/aal116/sub-019_acq-ep2ddtib3000tra64p2_dir-AP_space-T1w_desc-preproc_dwi.src.gz.odf.gqi.1.25.fib.trk.gz
Stdout:

Stderr:

Traceback:
        RuntimeError: subprocess exited with code 137.

241018-11:39:37,345 nipype.workflow INFO:
         [Node] Finished "calc_connectivity", elapsed time 672.381246s.
241018-11:39:37,348 nipype.workflow WARNING:
         Storing result file without outputs
...

the same happend with other atlases. Thanks for any help.

[tsalo]

Does the crash file contain any more information?

[samuelholly]

Hi, please see the attachment
crash-20241018-113939-root-calc_connectivity-a8780de8-dfa9-4579-bc35-aa391e15d81b.txt