plot_reports not removed from _KurtosisReconstructionInputSpec

[smeisler]

Summary

plot_reports is not getting removed from DKI workflow when skipping ODF plots

Additional details

• QSIRecon version: 1.0.0

What were you trying to do?

Run a big recon workflow (including DKI) while skipping ODF plots.

What did you expect to happen?

What actually happened?

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 268, 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 76, 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 298, in workflow_from_spec
    return init_dipy_dki_recon_wf(**kwargs)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/workflows/recon/dipy.py", line 616, in init_dipy_dki_recon_wf
    recon_dki = pe.Node(KurtosisReconstruction(**params), name="recon_dki")
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 567, in __init__
    super().__init__(
  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 '_KurtosisReconstructionInputSpec' object.

Reproducing the bug

singularity run --containall \
	--writable-tmpfs \
	-B ${PWD} \
	-B code/license.txt:/SGLR/FREESURFER_HOME/license.txt \
	containers/.datalad/environments/qsirecon-1-0-0/image \
	${PWD}/inputs/data/qsiprep/qsiprep \
	${PWD}/outputs/qsirecon \
	participant \
	-w ${PWD}/.git/tmp/wkdir \
	--fs-license-file /SGLR/FREESURFER_HOME/license.txt \
	-vv \
	--input-type qsiprep \
	--recon-spec ${PWD}/code/recon_spec.yaml \
	--output-resolution 1.5 \
	--nthreads $SLURM_CPUS_PER_TASK \
	--mem-mb $SLURM_MEM_PER_NODE \
	--participant-label "${subid}"

recon spec:

description: DKI, NODDI, MAPMRI, MSMT CSD, GQI Scalars, AutoTrack (with MSMT CSD)
name: workshop_recon_spec
space: T1w
nodes:

    # Run DKI from DIPY
-   action: DKI_reconstruction
    input: qsirecon
    name: dipy_dki
    parameters:
        write_fibgz: false
        write_mif: false
    qsirecon_suffix: DIPYDKI
    software: Dipy

    # Fit NODDI for WM and GM
-   action: fit_noddi
    input: qsirecon
    name: fit_noddi_wm
    parameters:
        dIso: 0.003
        dPar: 0.0017
        isExvivo: false
    qsirecon_suffix: wmNODDI
    software: AMICO
-   action: fit_noddi
    input: qsirecon
    name: fit_noddi_gm
    parameters:
        dIso: 0.003
        dPar: 0.0011
        isExvivo: false
    qsirecon_suffix: gmNODDI
    software: AMICO

    # Run MAPMRI
-   action: MAPMRI_reconstruction
    input: qsirecon
    name: mapmri_recon
    parameters:
        anisotropic_scaling: false
        bval_threshold: 2000
        dti_scale_estimation: false
        laplacian_regularization: true
        laplacian_weighting: 0.2
        radial_order: 6
        write_fibgz: false
        write_mif: false
    qsirecon_suffix: MAPMRI
    software: Dipy

    # Fit the actual GQI model to the data
-   action: reconstruction
    input: qsirecon
    name: dsistudio_gqi
    parameters:
        method: gqi
    qsirecon_suffix: DSIStudioGQI
    software: DSI Studio

    # Get 3D images of DSI Studio's scalar maps
-   action: export
    input: dsistudio_gqi
    name: gqi_scalars
    qsirecon_suffix: DSIStudioGQI
    software: DSI Studio

    # Perform the registration using the GQI-based QA+ISO
-   action: autotrack_registration
    input: dsistudio_gqi
    name: autotrack_gqi_registration
    # qsirecon_suffix: Don't include here - the map.gz is saved in autotrack
    software: DSI Studio

    # Run MSMT CSD
-   action: csd
    input: qsirecon
    name: msmt_csd
    parameters:
        fod:
            algorithm: msmt_csd
            max_sh:
            - 8
            - 8
            - 8
        mtnormalize: true
        response:
            algorithm: dhollander
    qsirecon_suffix: MSMTAutoTrack
    software: MRTrix3

    # Run Tractography
-   action: fod_fib_merge
    name: create_fod_fib
    # to include the fib file AND the map file
    input: autotrack_gqi_registration
    csd_input: msmt_csd
    # outputs include the FOD fib file and the map file is passed through
    qsirecon_suffix: MSMTAutoTrack
    parameters:
        model: msmt
-   action: autotrack
    input: create_fod_fib
    name: autotrack_fod
    parameters:
        tolerance: 22,26,30
        track_id: Association,Projection,Commissure,Cerebellum
        track_voxel_ratio: 2.0
        yield_rate: 1.0e-06
        model: msmt
    qsirecon_suffix: MSMTAutoTrack
    software: DSI Studio

    # Average scalars in bundles
-   action: bundle_map
    input: autotrack_fod
    name: bundle_means
    scalars_from:
    - gqi_scalars
    - dipy_dki
    - mapmri_recon
    - fit_noddi_wm
    software: qsirecon

    # Map scalars to MNI
-   action: template_map
    input: qsirecon
    name: template_map
    parameters:
        interpolation: NearestNeighbor
    scalars_from:
    - gqi_scalars
    - dipy_dki
    - mapmri_recon
    - fit_noddi_wm
    - fit_noddi_gm
    software: qsirecon