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ENH: Allow retrieving T2w
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mgxd committed Dec 11, 2024
1 parent bef4e76 commit f260c49
Showing 1 changed file with 9 additions and 1 deletion.
10 changes: 9 additions & 1 deletion smriprep/interfaces/templateflow.py
Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@
InputMultiObject,
SimpleInterface,
TraitedSpec,
Undefined,
isdefined,
traits,
)
Expand All @@ -51,6 +52,7 @@ class _TemplateFlowSelectInputSpec(BaseInterfaceInputSpec):
class _TemplateFlowSelectOutputSpec(TraitedSpec):
t1w_file = File(exists=True, desc='T1w template')
brain_mask = File(exists=True, desc="Template's brain mask")
t2w_file = File(desc='T2w template')


class TemplateFlowSelect(SimpleInterface):
Expand All @@ -72,6 +74,8 @@ class TemplateFlowSelect(SimpleInterface):
>>> result = select.run()
>>> result.outputs.t1w_file # doctest: +ELLIPSIS
'.../tpl-MNIPediatricAsym_cohort-5_res-1_T1w.nii.gz'
>>> result.outputs.t2w_file # doctest: +ELLIPSIS
'.../tpl-MNIPediatricAsym_cohort-5_res-1_T2w.nii.gz'
>>> select = TemplateFlowSelect(resolution=2)
>>> select.inputs.template = 'MNIPediatricAsym:cohort-5'
Expand All @@ -93,7 +97,8 @@ class TemplateFlowSelect(SimpleInterface):
>>> result = select.run()
>>> result.outputs.t1w_file # doctest: +ELLIPSIS
'.../tpl-MNI305_T1w.nii.gz'
>>> result.outputs.t2w_file
<undefined>
"""

input_spec = _TemplateFlowSelectInputSpec
Expand All @@ -111,6 +116,7 @@ def _run_interface(self, runtime):
files = fetch_template_files(self.inputs.template, specs)
self._results['t1w_file'] = files['t1w']
self._results['brain_mask'] = files['mask']
self._results['t2w_file'] = files['t2w']
return runtime


Expand Down Expand Up @@ -206,4 +212,6 @@ def fetch_template_files(
files['mask'] = tf.get(name[0], desc='brain', suffix='mask', **specs) or tf.get(
name[0], label='brain', suffix='mask', **specs
)
# Not guaranteed to exist so add fallback
files['t2w'] = tf.get(name[0], desc=None, suffix='T2w', **specs) or Undefined
return files

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