QSIRecon issue with dsi_studio_gqi

[neurotix93]

Hello,

version: 2.3.0
OS: Ubuntu 22.04.5

I am currently trying out the DWI pre processing built into TI Toolbox.
QSIPrep seems to have run well without issue. However, now I am trying to run QSIRecon with dsi_studio_gqi.

I am running into this error:
260324-23:06:29,97 nipype.workflow IMPORTANT:
Building QSIRecon's workflow:

• BIDS dataset path: /data.
• Participant list: ['002'].
• Run identifier: 20260324-230622_5e6ea3b7-6569-4026-a7e3-289626886945.
  260324-23:06:30,254 nipype.utils INFO:
  Collected anatomical data:
  acpc_aparc: null
  acpc_aseg: /data/sub-002/anat/sub-002_space-ACPC_desc-aseg_dseg.nii.gz
  acpc_brain_mask: /data/sub-002/anat/sub-002_space-ACPC_desc-brain_mask.nii.gz
  acpc_csf_probseg: null
  acpc_gm_probseg: null
  acpc_preproc: /data/sub-002/anat/sub-002_space-ACPC_desc-preproc_T1w.nii.gz
  acpc_seg: /data/sub-002/anat/sub-002_space-ACPC_dseg.nii.gz
  acpc_to_template_xfm: /data/sub-002/anat/sub-002_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5
  acpc_wm_probseg: null
  orig_to_acpc_xfm: null
  template_to_acpc_xfm: /data/sub-002/anat/sub-002_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5
  260324-23:06:30,255 nipype.workflow INFO:
  Anatomical data available for /data/sub-002/anat/sub-002_space-ACPC_desc-preproc_T1w.nii.gz:
  acpc_aparc: null
  acpc_aseg: /data/sub-002/anat/sub-002_space-ACPC_desc-aseg_dseg.nii.gz
  acpc_brain_mask: /data/sub-002/anat/sub-002_space-ACPC_desc-brain_mask.nii.gz
  acpc_csf_probseg: null
  acpc_gm_probseg: null
  acpc_preproc: /data/sub-002/anat/sub-002_space-ACPC_desc-preproc_T1w.nii.gz
  acpc_seg: /data/sub-002/anat/sub-002_space-ACPC_dseg.nii.gz
  acpc_to_template_xfm: /data/sub-002/anat/sub-002_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5
  acpc_wm_probseg: null
  orig_to_acpc_xfm: null
  template_to_acpc_xfm: /data/sub-002/anat/sub-002_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5
  260324-23:06:30,256 nipype.workflow INFO:
  Found high-res anatomical data in preprocessed inputs for 002.
  260324-23:06:30,256 nipype.workflow INFO:
  acpc_aparc (): None ()
  260324-23:06:30,256 nipype.workflow INFO:
  acpc_seg (): /data/sub-002/anat/sub-002_space-ACPC_dseg.nii.gz ()
  260324-23:06:30,256 nipype.workflow INFO:
  acpc_aseg (): /data/sub-002/anat/sub-002_space-ACPC_desc-aseg_dseg.nii.gz ()
  260324-23:06:30,256 nipype.workflow INFO:
  acpc_brain_mask (): /data/sub-002/anat/sub-002_space-ACPC_desc-brain_mask.nii.gz ()
  260324-23:06:30,256 nipype.workflow INFO:
  acpc_preproc (): /data/sub-002/anat/sub-002_space-ACPC_desc-preproc_T1w.nii.gz ()
  260324-23:06:30,256 nipype.workflow INFO:
  acpc_csf_probseg (): None ()
  260324-23:06:30,257 nipype.workflow INFO:
  acpc_gm_probseg (): None ()
  260324-23:06:30,257 nipype.workflow INFO:
  acpc_wm_probseg (): None ()
  260324-23:06:30,257 nipype.workflow INFO:
  orig_to_acpc_xfm (): None ()
  260324-23:06:30,257 nipype.workflow INFO:
  template_to_acpc_xfm (): /data/sub-002/anat/sub-002_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5 ()
  260324-23:06:30,257 nipype.workflow INFO:
  acpc_to_template_xfm (): /data/sub-002/anat/sub-002_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5 ()
  260324-23:06:30,298 nipype.interface WARNING:
  No atlas images found for Schaefer100 with query {'space': 'MNI152NLin2009cAsym', 'suffix': 'dseg', 'extension': ['.nii.gz', '.nii']}
  260324-23:06:30,298 nipype.workflow INFO:
  Found 2 high-res anatomicals to process
  260324-23:06:30,302 nipype.workflow INFO:
  Found T1w-to-template transforms from QSIRecon
  260324-23:06:30,304 nipype.workflow INFO:
  Transforming ODF ROIs into DWI space for visual report.
  260324-23:06:30,307 nipype.workflow INFO:
  skipping ODF plots for dsistudio_gqi
  260324-23:06:30,310 nipype.workflow INFO:
  skipping ODF plots for scalar_export
  260324-23:06:30,322 nipype.workflow INFO:
  skipping ODF plots for tractography
  Process Process-2:
  Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
  self.run()
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/process.py", line 108, in run
  self._target(*self._args, **self._kwargs)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/cli/workflow.py", line 133, in build_workflow
  retval["workflow"] = init_qsirecon_wf()
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/workflows/base.py", line 44, in init_qsirecon_wf
  single_subject_wf = init_single_subject_recon_wf(subject_id=subject_id)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/workflows/base.py", line 275, in init_single_subject_recon_wf
  dwi_recon_wfs[dwi_file] = init_dwi_recon_workflow(
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/workflows/recon/build_workflow.py", line 86, in init_dwi_recon_workflow
  new_node = workflow_from_spec(
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/workflows/recon/build_workflow.py", line 285, in workflow_from_spec
  return init_dsi_studio_tractography_wf(**kwargs)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/workflows/recon/dsi_studio.py", line 242, in init_dsi_studio_tractography_wf
  DSIStudioTracking(num_threads=omp_nthreads, **params),
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 633, in init
  super().init(**inputs)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 204, in init
  self.inputs.trait_set(**inputs)
  File "/opt/conda/envs/qsiprep/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 'plot_reports' attribute of a 'DSIStudioTrackingInputSpec' object.
  Traceback (most recent call last):
  File "", line 198, in _run_module_as_main
  File "", line 88, in _run_code
  File "/ti-toolbox/tit/pre/main.py", line 43, in
  main()
  File "/ti-toolbox/tit/pre/main.py", line 23, in main
  exit_code = run_pipeline(
  ^^^^^^^^^^^^^
  File "/ti-toolbox/tit/pre/structural.py", line 409, in run_pipeline
  _run_subject_pipeline(
  File "/ti-toolbox/tit/pre/structural.py", line 166, in _run_subject_pipeline
  _run_step(
  File "/ti-toolbox/tit/pre/structural.py", line 30, in _run_step
  func()
  File "/ti-toolbox/tit/pre/structural.py", line 168, in
  lambda: run_qsirecon(
  ^^^^^^^^^^^^^
  File "/ti-toolbox/tit/pre/qsi/qsirecon.py", line 165, in run_qsirecon
  raise PreprocessError(f"QSIRecon {spec} failed with exit code {returncode}")
  tit.pre.utils.PreprocessError: QSIRecon dsi_studio_gqi failed with exit code 1
  Process returned non-zero exit code (1)

It seems QSI Recon is trying to set a plot_reports parameter on DSI Studio's tractography interface that doesn't exist in the version installed in the container. Would you have any advice to solve this issue?

[idossha]

Hi @neurotix93,

QSIRecon's dsi_studio_gqi recon spec includes a tractography step that passes a plot_reports parameter to the DSIStudioTracking nipype interface, but I think the parameter doesn't exist in the interface definition. The crash happens entirely inside QSIRecon's own code (qsirecon/workflows/recon/dsi_studio.py:242), before any TI-Toolbox code is involved beyond launching the container.

1. Try a newer QSIRecon version. It seems like their latest release is 1.2.0 which you can change within the toolbox and it will call the newer version. Maybe they fixed it there.

2. Try a different recon spec as a workaround. Mrtrix_multishell_msmt_ACT-fast (the default) or multishell_scalarfest may work without this bug.

3. File an issue upstream at https://github.com/PennLINC/qsirecon if one doesn't already exist for this plot_reports trait error.

[neurotix93]

Hello, I will try out 1.2.0 :) I can't use the multishell recon specs, as I only acquired single shell diffusion data.
Thanks so much for looking into it. It's quite important as we are trying to get a study started, and the last thing to do is to ensure we have the simulation pipeline all set up before starting. I am testing out lots of different things, on pilot subject data we collected.

[neurotix93]

Seems like some progress was made when I changed to 1.2.0, but still running into an issue (have tried with both dsi_studio_gqi and dipy_dki):

Starting QSIRecon for subject 002 with specs: ['dsi_studio_gqi'], atlases: ['AAL116', 'Schaefer100']
Running QSIRecon spec: dsi_studio_gqi
Running QSIRecon dsi_studio_gqi for subject 002...
usage: qsirecon [-h]
[--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[--session-id SESSION_ID [SESSION_ID ...]]
[-d PACKAGE=PATH [PACKAGE=PATH ...]] [--bids-filter-file FILE]
[--bids-database-dir PATH] [--nprocs NPROCS]
[--omp-nthreads OMP_NTHREADS] [--mem MEMORY_MB] [--low-mem]
[--use-plugin FILE] [--sloppy] [--boilerplate-only]
[--reports-only]
[--report-output-level {root,subject,session}] [--infant]
[--b0-threshold B0_THRESHOLD]
[--output-resolution OUTPUT_RESOLUTION]
[--fs-license-file PATH] [--recon-spec RECON_SPEC]
[--input-type {qsiprep,ukb,hcpya}] [--fs-subjects-dir PATH]
[--skip-odf-reports]
[--recon-spec-aux-files RECON_SPEC_AUX_FILES]
[--atlases ATLAS [ATLAS ...]] [--version] [-v] [-w WORK_DIR]
[--resource-monitor] [--config-file FILE] [--write-graph]
[--stop-on-first-crash] [--notrack]
[--debug {pdb,all} [{pdb,all} ...]]
input_dir output_dir {participant}
qsirecon: error: Path should point to a file (or symlink of file): .
Traceback (most recent call last):
File "", line 198, in _run_module_as_main
File "", line 88, in _run_code
File "/ti-toolbox/tit/pre/main.py", line 43, in
main()
File "/ti-toolbox/tit/pre/main.py", line 23, in main
exit_code = run_pipeline(
^^^^^^^^^^^^^
File "/ti-toolbox/tit/pre/structural.py", line 409, in run_pipeline
_run_subject_pipeline(
File "/ti-toolbox/tit/pre/structural.py", line 166, in _run_subject_pipeline
_run_step(
File "/ti-toolbox/tit/pre/structural.py", line 30, in _run_step
func()
File "/ti-toolbox/tit/pre/structural.py", line 168, in
lambda: run_qsirecon(
^^^^^^^^^^^^^
File "/ti-toolbox/tit/pre/qsi/qsirecon.py", line 165, in run_qsirecon
raise PreprocessError(f"QSIRecon {spec} failed with exit code {returncode}")
tit.pre.utils.PreprocessError: QSIRecon dsi_studio_gqi failed with exit code 2
Process returned non-zero exit code (1)

[idossha]

I am looking into it. I may have some insight in a few hours.

[idossha]

I may have found a workaround this issue. I am testing it now locally, will get back to you when I see the results.

[neurotix93]

That's great, thanks a lot.