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Merge branch 'main' into improve-reports
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@tsalo
tsalo committed Aug 16, 2024
2 parents c02cc64 + 2eae1a4 commit e127aba
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Showing 5 changed files with 23 additions and 68 deletions.
26 changes: 15 additions & 11 deletions qsirecon/interfaces/pyafq.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ class PyAFQInputSpec(BaseInterfaceInputSpec):
itk_file = File(exists=True, mandatory=True)
kwargs = traits.Dict(exists=True, mandatory=True)
tck_file = traits.Either(None, File(exists=True))
n_procs = traits.Int(1, usedefault=True)


class PyAFQOutputSpec(TraitedSpec):
Expand Down Expand Up @@ -79,19 +80,22 @@ def _run_interface(self, runtime):
if brain_mask_definition is None:
brain_mask_definition = kwargs["brain_mask_definition"]
kwargs.pop("brain_mask_definition", None)
# if itk_map is None: # Use pyAFQ internal mapping
# itk_map = kwargs['mapping_definition']
# kwargs.pop('mapping_definition', None)

if "parallel_segmentation" in kwargs:
if (
"n_jobs" not in kwargs["parallel_segmentation"]
or kwargs["parallel_segmentation"]["n_jobs"] == -1
):
kwargs["parallel_segmentation"]["n_jobs"] = self.inputs.kwargs["omp_nthreads"]

# if "parallel_segmentation" in kwargs:
# if (
# "n_jobs" not in kwargs["parallel_segmentation"]
# or kwargs["parallel_segmentation"]["n_jobs"] == -1
# ):
# kwargs["parallel_segmentation"]["n_jobs"] = self.inputs.kwargs["omp_nthreads"]
# else:
# kwargs["parallel_segmentation"] = {}
# kwargs["parallel_segmentation"]["n_jobs"] = self.inputs.kwargs["omp_nthreads"]

if self.inputs.n_procs > 1:
kwargs["parallel_segmentation"]["n_jobs"] = self.inputs.n_procs
else:
kwargs["parallel_segmentation"] = {}
kwargs["parallel_segmentation"]["n_jobs"] = self.inputs.kwargs["omp_nthreads"]
kwargs["parallel_segmentation"]["n_jobs"] = self.inputs.n_procs

output_dir = shim_dir + "/PYAFQ/"
os.makedirs(output_dir, exist_ok=True)
Expand Down
26 changes: 0 additions & 26 deletions qsirecon/tests/data/pyafq_recon_external_trk_outputs.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -38,26 +38,6 @@ qsirecon-PYAFQ/sub-ABCD.html
qsirecon-PYAFQ/sub-ABCD/dwi
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuateend0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuateend0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuateinclude0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuateinclude0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuateinclude1_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuateinclude1_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuateprob_map0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuateprob_map0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuatestart0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuatestart0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalend0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalend0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalinclude0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalinclude0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalinclude1_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalinclude1_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalprob_map0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalprob_map0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalstart0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalstart0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftSuperiorLongitudinalend0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftSuperiorLongitudinalend0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftSuperiorLongitudinalexclude0_mask.json
Expand All @@ -81,9 +61,6 @@ qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-RightCorticospinalstart0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-RightCorticospinalstart0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/bundles
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftArcuate_tractography.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftCorticospinal_tractography.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftCorticospinal_tractography.trk
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftSuperiorLongitudinal_tractography.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftSuperiorLongitudinal_tractography.trk
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-RightCorticospinal_tractography.json
Expand Down Expand Up @@ -122,11 +99,8 @@ qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/sub-ABCD_acq-
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/sub-ABCD_acq-10per000_space-template_desc-b0_dwi.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/sub-ABCD_acq-10per000_space-template_desc-b0_dwi.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_bundles
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftArcuateviz_dwi.html
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftCorticospinalviz_dwi.html
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftSuperiorLongitudinalviz_dwi.html
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-RightCorticospinalviz_dwi.html
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_core_bundles
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_core_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftCorticospinalviz_dwi.html
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_core_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftSuperiorLongitudinalviz_dwi.html
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_core_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-RightCorticospinalviz_dwi.html
25 changes: 0 additions & 25 deletions qsirecon/tests/data/pyafq_recon_full_outputs.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -16,26 +16,6 @@ qsirecon-PYAFQ/sub-ABCD.html
qsirecon-PYAFQ/sub-ABCD/dwi
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuateend0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuateend0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuateinclude0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuateinclude0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuateinclude1_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuateinclude1_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuateprob_map0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuateprob_map0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuatestart0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftArcuatestart0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalend0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalend0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalinclude0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalinclude0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalinclude1_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalinclude1_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalprob_map0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalprob_map0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalstart0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftCorticospinalstart0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftSuperiorLongitudinalend0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftSuperiorLongitudinalend0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-LeftSuperiorLongitudinalexclude0_mask.json
Expand All @@ -59,9 +39,6 @@ qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-RightCorticospinalstart0_mask.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/ROIs/sub-ABCD_acq-10per000_space-subject_desc-RightCorticospinalstart0_mask.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/bundles
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftArcuate_tractography.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftCorticospinal_tractography.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftCorticospinal_tractography.trk
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftSuperiorLongitudinal_tractography.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftSuperiorLongitudinal_tractography.trk
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-RightCorticospinal_tractography.json
Expand Down Expand Up @@ -106,11 +83,9 @@ qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/sub-ABCD_acq-
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/sub-ABCD_acq-10per000_space-template_desc-b0_dwi.json
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/sub-ABCD_acq-10per000_space-template_desc-b0_dwi.nii.gz
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_bundles
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftCorticospinalviz_dwi.html
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftSuperiorLongitudinalviz_dwi.html
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-RightCorticospinalviz_dwi.html
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_core_bundles
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_core_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftCorticospinalviz_dwi.html
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_core_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftSuperiorLongitudinalviz_dwi.html
qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_core_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-RightCorticospinalviz_dwi.html
sub-ABCD
8 changes: 4 additions & 4 deletions qsirecon/utils/sloppy_recon.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,10 +29,10 @@ def make_sloppy(spec):
("MRTrix3", "connectivity"): {"tck2connectome": {"search_radius": "DELETE"}},
("MRTrix3", "global_tractography"): {"niters": 10000},
("pyAFQ", "pyafq_tractometry"): {
"mapping_definition": 'AffMap(affine_kwargs={"level_iters": [10, 10, 10]})',
"bundle_info": 'default18_bd()["Left Superior Longitudinal", "Left Arcuate", '
'"Left Corticospinal", "Right Corticospinal"]',
"n_seeds": 10000,
"mapping_definition": 'AffMap(affine_kwargs={"pipeline": ["center_of_mass"]})',
"bundle_info": 'default18_bd()["Left Superior Longitudinal", '
'"Right Corticospinal"]',
"n_seeds": 1000,
"random_seeds": True,
"export": "all_bundles_figure",
},
Expand Down
6 changes: 4 additions & 2 deletions qsirecon/workflows/recon/pyafq.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -68,10 +68,12 @@ def init_pyafq_wf(available_anatomical_data, name="afq", qsirecon_suffix="", par
niu.IdentityInterface(fields=["afq_dir", "recon_scalars"]), name="outputnode"
)
outputnode.inputs.recon_scalars = []

omp_nthreads = config.nipype.omp_nthreads
kwargs = _parse_qsirecon_params_dict(params)
kwargs["omp_nthreads"] = config.nipype.omp_nthreads
run_afq = pe.Node(PyAFQRecon(kwargs=kwargs), name="run_afq")
run_afq = pe.Node(
PyAFQRecon(kwargs=kwargs, n_procs=omp_nthreads), name="run_afq", n_procs=omp_nthreads
)
workflow = pe.Workflow(name=name)
if params.get("use_external_tracking", False):
workflow.connect([
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