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pyAFQ pipeline: Use previous analysis derivatives as inputs for masks: seed and brain. #571

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pyAFQ pipeline: Use previous analysis derivatives as inputs for masks: seed and brain. #571

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497fa40
Use previous analysis derivatives as inputs for masks: seed and brain.
arokem May 12, 2023
050716f
Now I am thinking that maybe this is what we need for the WM prob map.
arokem May 12, 2023
cf425cd
Do this the right way, by hooking up pyAFQ to qsiprep outputs.
arokem May 12, 2023
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9 changes: 4 additions & 5 deletions qsiprep/data/pipelines/pyafq_tractometry.json
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Original file line number Diff line number Diff line change
Expand Up @@ -16,13 +16,13 @@
"directions": "prob",
"max_angle": 30.0,
"sphere": "",
"seed_mask": "",
"seed_threshold": 0,
"seed_mask": "WM_probseg",
"seed_threshold": 0.5,
"n_seeds": 1,
"random_seeds": false,
"rng_seed": "",
"stop_mask": "",
"stop_threshold": 0,
"stop_mask": "WM_probseg",
"stop_threshold": 0.5,
"step_size": 0.5,
"min_length": 50,
"max_length": 250,
Expand Down Expand Up @@ -67,7 +67,6 @@
"csd_lambda_": 1,
"csd_tau": 0.1,
"gtol": 0.01,
"brain_mask_definition": "",
"bundle_info": "",
"reg_template_spec": "mni_T1",
"mapping_definition": "",
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25 changes: 20 additions & 5 deletions qsiprep/interfaces/pyafq.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@ class PyAFQInputSpec(BaseInterfaceInputSpec):
bvec_file = File(exists=True, mandatory=True)
dwi_file = File(exists=True, mandatory=True)
mask_file = File(exists=True, mandatory=True)
wm_mask_file = File(exists=True, mandatory=True)
itk_file = File(exists=True, mandatory=True)
kwargs = traits.Dict(exists=True, mandatory=True)
tck_file = traits.Either(None, File(exists=True))
Expand All @@ -56,31 +57,44 @@ def _run_interface(self, runtime):
newpath=shim_dir)
mask_file = fname_presuffix(self.inputs.mask_file,
newpath=shim_dir)
wm_mask_file = fname_presuffix(self.inputs.wm_mask_file,
newpath=shim_dir)
itk_file = fname_presuffix(self.inputs.itk_file,
newpath=shim_dir)
os.symlink(self.inputs.bval_file, bval_file)
os.symlink(self.inputs.bvec_file, bvec_file)
os.symlink(self.inputs.dwi_file, dwi_file)
os.symlink(self.inputs.mask_file, mask_file)
os.symlink(self.inputs.itk_file, itk_file)

os.symlink(self.inputs.wm_mask_file, wm_mask_file)
kwargs = self.inputs.kwargs

if self.inputs.tck_file and isdefined(self.inputs.tck_file):
tck_file = fname_presuffix(self.inputs.tck_file,
newpath=shim_dir)
newpath=shim_dir)
os.symlink(self.inputs.tck_file, tck_file)
else:
tck_file = None

brain_mask_definition = ImageFile(path=mask_file)
itk_map = ItkMap(warp_path=itk_file)
seed_mask_definition = ImageFile(path=wm_mask_file)
stop_mask_definition = ImageFile(path=wm_mask_file)

# XXX Make ItkMap work at some point
# itk_map = ItkMap(warp_path=itk_file)

if tck_file is None:
tck_file = kwargs['import_tract']
kwargs.pop('import_tract', None)
if brain_mask_definition is None:
brain_mask_definition = kwargs['brain_mask_definition']
kwargs.pop('brain_mask_definition', None)

tracking_params = kwargs.pop('tracking_params', None)
if tracking_params is not None:
if tracking_params["seed_mask"] == "WM_prob":
tracking_params["seed_mask"] = seed_mask_definition
if tracking_params["stop_mask"] == "WM_prob":
tracking_params["stop_mask"] = stop_mask_definition

# if itk_map is None: # Use pyAFQ internal mapping
# itk_map = kwargs['mapping_definition']
# kwargs.pop('mapping_definition', None)
Expand All @@ -100,6 +114,7 @@ def _run_interface(self, runtime):
import_tract=tck_file,
brain_mask_definition=brain_mask_definition,
# mapping_definition=itk_map,
tracking_params=tracking_params,
**kwargs)

if "export" not in kwargs or kwargs["export"] == "all":
Expand Down
1 change: 1 addition & 0 deletions qsiprep/workflows/recon/pyafq.py
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Expand Up @@ -79,6 +79,7 @@ def init_pyafq_wf(omp_nthreads, available_anatomical_data,
('bval_file', 'bval_file'),
('bvec_file', 'bvec_file'),
('dwi_mask', 'mask_file'),
('wm_mask', 'wm_mask_file'),
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@mattcieslak : what should we put here for wm_mask?

('t1_2_mni_reverse_transform', 'itk_file')]),
(run_afq, outputnode, [('afq_dir', 'afq_dir')])
])
Expand Down