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kaitjnx10
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Update anat save for new orchestration
1 parent 014b17a commit ba0acfb

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Lines changed: 4 additions & 1 deletion

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src/rbc/bids/anatomical.py

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Original file line numberDiff line numberDiff line change
@@ -83,3 +83,5 @@ def export_anatomical(anat: Bids, outputs: AnatomicalOutputs) -> None:
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"mode": "image",
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},
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)
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mni = anat.derive(space=TemplateSpace.MNI152NLIN6ASYM)
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mni.save(outputs.brain_tpl, suffix=Suffix.T1W, desc="brain")

tests/unit/bids/test_exports.py

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Original file line numberDiff line numberDiff line change
@@ -42,6 +42,7 @@ def _make_anat_outputs(w: Path) -> AnatomicalOutputs:
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return AnatomicalOutputs(
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brain=_dummy(w, "brain.nii.gz"),
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brain_mask=_dummy(w, "brain_mask.nii.gz"),
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brain_tpl=_dummy(w, "brain_tpl.nii.gz"),
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csf_mask=_dummy(w, "csf_mask.nii.gz"),
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gm_mask=_dummy(w, "gm_mask.nii.gz"),
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wm_mask=_dummy(w, "wm_mask.nii.gz"),
@@ -134,7 +135,7 @@ def test_creates_8_files(
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outputs = _make_anat_outputs(workdir)
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export_anatomical(anat_bids, outputs)
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saved = list(pipe_ctx.output_dir.rglob("*.*"))
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assert len(saved) == 8
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assert len(saved) == 9
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def test_filenames_contain_expected_entities(
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self, anat_bids: Bids, workdir: Path, pipe_ctx: RunContext

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