Crash during connectivity matrix

Software Support
1

Summary of what happened:

Hello,

I encountered the following error while running qsirecon on qsiprepped data.

Command used (and if a helper script was used, a link to the helper script or the command generated):

Below is the command I used:

docker run -ti --rm \
  -v /data/bids/derivatives/qsiprep:/data/qsiprep \
  -v /data/bids/derivatives/qsirecon:/data/qsirecon \
  -v /home/user/license.txt:/opt/freesurfer/license.txt:ro \
  pennlinc/qsirecon:latest \
  /data/qsiprep /data/qsirecon participant \
  --participant-label 11107 \
  --fs-license-file /opt/freesurfer/license.txt \
  --recon-spec dsi_studio_gqi \
  --atlases 4S156Parcels 4S256Parcels 4S456Parcels

Version:

1.1.1

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):

This is from the crash log:

Node: qsirecon_1_1_wf.sub-11107_dsistudio_pipeline.sub_11107_dir_AP_space_ACPC_desc_preproc_recon_wf.streamline_connectivity.calc_connectivity
Working directory: /tmp/work/qsirecon_1_1_wf/sub-11107_dsistudio_pipeline/sub_11107_dir_AP_space_ACPC_desc_preproc_recon_wf/streamline_connectivity/calc_connectivity

Node inputs:

args = <undefined>
atlas_configs = <undefined>
atlas_labels_file = <undefined>
atlas_name = <undefined>
connectivity = <undefined>
connectivity_type = pass,end
connectivity_value = count,ncount,mean_length,gfa
environ = {}
fa_threshold = <undefined>
fiber_count = <undefined>
initial_dir = <undefined>
input_fib = <undefined>
interpo_angle = <undefined>
interpolation = <undefined>
max_length = <undefined>
min_length = <undefined>
num_threads = 8
random_seed = <undefined>
seed_count = <undefined>
seed_file = <undefined>
seed_plan = <undefined>
smoothing = <undefined>
step_size = <undefined>
thread_count = 1
to_export = <undefined>
trk_file = <undefined>
turning_angle = <undefined>

Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 66, 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 525, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/qsiprep/lib/python3.10/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 calc_connectivity.

Traceback:
	Traceback (most recent call last):
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 401, in run
	    runtime = self._run_interface(runtime)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/interfaces/dsi_studio.py", line 453, in _run_interface
	    wf_result = workflow.run(**plugin_settings)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/workflows.py", line 625, in run
	    runner.run(execgraph, updatehash=updatehash, config=self.config)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/base.py", line 177, in run
	    self._clean_queue(jobid, graph, result=result)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/base.py", line 255, in _clean_queue
	    raise RuntimeError("".join(result["traceback"]))
	RuntimeError: Traceback (most recent call last):
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 66, 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 525, in run
	    result = self._run_interface(execute=True)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
	    return self._run_command(execute)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/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 4S156Parcels.

	Cmdline:
		dsi_studio --action=ana  --connectivity=/data/qsirecon/sub-11107/dwi/sub-11107_dir-AP_space-ACPC_seg-4S156Parcels_dseg.nii.gz --connectivity_type=pass,end --connectivity_value=count,ncount,mean_length,gfa --source=/tmp/work/qsirecon_1_1_wf/sub-11107_dsistudio_pipeline/sub_11107_dir_AP_space_ACPC_desc_preproc_recon_wf/streamline_connectivity/calc_connectivity/dsistudio_atlasgraph/4S156Parcels/sub-11107_dir-AP_space-ACPC_desc-preproc_dwi.src.gz.odf.gqi.1.25.fib.gz --thread_count=1 --thread_count=1 --tract=/tmp/work/qsirecon_1_1_wf/sub-11107_dsistudio_pipeline/sub_11107_dir_AP_space_ACPC_desc_preproc_recon_wf/streamline_connectivity/calc_connectivity/dsistudio_atlasgraph/4S156Parcels/sub-11107_dir-AP_space-ACPC_desc-preproc_dwi.src.gz.odf.gqi.1.25.fib.trk.gz
	Stdout:

	Stderr:

	Traceback:
		Traceback (most recent call last):
		  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 402, in run
		    runtime = self._post_run_hook(runtime)
		  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/interfaces/dsi_studio.py", line 359, in _post_run_hook
		    _sanitized_connectivity_matrix(matfile, official_labels)
		  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/interfaces/dsi_studio.py", line 516, in _sanitized_connectivity_matrix
		    matfile_region_ids = np.array([int(name.split("_")[-1]) for name in column_names])
		  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/interfaces/dsi_studio.py", line 516, in <listcomp>
		    matfile_region_ids = np.array([int(name.split("_")[-1]) for name in column_names])
		ValueError: invalid literal for int() with base 10: 'LH-Pu'

Screenshots / relevant information:

3

Hi @Catherine_Tang,

As a test, may you try rolling back to version 1.1.0?

Best,
Steven

4

Hi Steven,

I can confirm that reversing back to 1.1.1 worked. Is this a bug?

Thanks

5

Hi @Catherine_Tang,

Do you mean 1.1.1 or 1.1.0?

Best,
Steven

6

I actually put in 1.1.0 in my command, but in the command window it pulled 1.1.1 from github so I’m not entirely sure which version it pulled.

7

just went into the output html:
QSIRecon version: 1.1.1.dev0+gaf43da9.d20250414

8

Then you used 1.1.0, the weird dev stuff is just a little bug in how versions are reported.

We’re working on a fix now for this in next release, so for now if 1.1.0 works for you stick with that.

Best,
Steven

1 Like