I’m trying to run csdsi_3dshore on some qsiprep outputs, using this commmand:
apptainer run --containall --cleanenv -B /mystudy/bids:/bids -B /mystudy/output_csdsi:/output -B /mystudy/work_csdsi_recon:/work -B freesurfer_license.txt:/opt/freesurfer/license.txt qsiprep_latest.sif /bids /output participant --fs-license-file /opt/freesurfer/license.txt --freesurfer-input=/bids/derivatives/freesurfer --work-dir=/work --output-resolution 1.8 --recon-spec=csdsi_3dshore --recon-only --recon-input=/output/qsiprep --write-graph
and I get the following error:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/usr/local/miniconda/lib/python3.10/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.10/site-packages/qsiprep/cli/run.py", line 1215, in build_recon_workflow
retval['workflow'] = init_qsirecon_wf(
File "/usr/local/miniconda/lib/python3.10/site-packages/qsiprep/workflows/recon/base.py", line 99, in init_qsirecon_wf
single_subject_wf = init_single_subject_wf(
File "/usr/local/miniconda/lib/python3.10/site-packages/qsiprep/workflows/recon/base.py", line 272, in init_single_subject_wf
dwi_recon_wfs[dwi_file] = init_dwi_recon_workflow(
File "/usr/local/miniconda/lib/python3.10/site-packages/qsiprep/workflows/recon/build_workflow.py", line 50, in init_dwi_recon_workflow
new_node = workflow_from_spec(
File "/usr/local/miniconda/lib/python3.10/site-packages/qsiprep/workflows/recon/build_workflow.py", line 153, in workflow_from_spec
return init_dsi_studio_connectivity_wf(**kwargs)
File "/usr/local/miniconda/lib/python3.10/site-packages/qsiprep/workflows/recon/dsi_studio.py", line 408, in init_dsi_studio_connectivity_wf
DSIStudioAtlasGraph(num_threads=omp_nthreads, **params),
File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 563, in __init__
super(SimpleInterface, self).__init__(
File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 202, in __init__
self.inputs.trait_set(**inputs)
File "/usr/local/miniconda/lib/python3.10/site-packages/traits/has_traits.py", line 1520, in trait_set
setattr(self, name, value)
traits.trait_errors.TraitError: Cannot set the undefined 'output_trk' attribute of a 'DSIStudioAtlasGraphInputSpec' object.
I see some references to others with the same error, but the fix provided didn’t solve the problem. I did notice that in the csdsi_3dshore.json qsiprep/qsiprep/data/pipelines/csdsi_3dshore.json at master · PennLINC/qsiprep · GitHub, the node list includes:
"nodes": [
{"name": "csdsi_3dshore", "software": "Dipy", "action": "3dSHORE_reconstruction", "input": "qsiprep", "output_suffix": "3dSHORE", .... },
{"name": "streamline_connectivity", "software": "DSI Studio", "action": "connectivity", "input": "csdsi_3dshore", ... },
{"name": "controlability", "input": "streamline_connectivity", "action": "controllability", "output_suffix": "rec-3dshore_control", ... },
{"name": "msmt_csd", "software": "MRTrix3", "action": "csd", "output_suffix": "msmtcsd", "input":"csdsi_3dshore", ... }
... [some more mrtrix steps]
]
The error seems to come from the streamline_connectivity step. I’m new to qsiprep, but I’m confused about what the streamline_connectivity and controlability nodes do in this case. The streamline_connectivity seems to be a node that would run AFTER dsi_studio tractography, which is not being run here at all. And I’m not sure what the controlability node means at all.
If I create a custom .json without those two nodes, the pipeline runs. (running mrtrix3 tckgen now… presumably it will complete).
Are those two nodes needed for something? If this is just a bug, I’m happy to submit a PR. I’m just not sure if I’m missing something.