ENH: Add helper script to test workflow

Author: mgxd

scripts/bold_subcortical.py

@@ -0,0 +1,64 @@
+"""Script for testing the subcortical MNI alignment"""
+from pathlib import Path
+
+
+def init_workflow(bold_file, bold_roi, bold_atlas_roi, atlas_xfm, TR=None):
+    from nibabies.workflows.bold.alignment import init_subcortical_mni_alignment_wf
+
+    if TR is None:
+        # guess TR from header
+        import nibabel as nb
+        img = nb.load(bold_file)
+        assert len(img.shape) > 3, "Not a 4D file"
+        TR = img.header['pixdim'][4]
+
+    wf = init_subcortical_mni_alignment_wf(repetition_time=TR)
+    wf.inputs.inputnode.bold_file = bold_file
+    wf.inputs.inputnode.bold_roi = bold_roi
+    wf.inputs.inputnode.atlas_roi = bold_atlas_roi
+    wf.inputs.inputnode.atlas_xfm = atlas_xfm
+
+    wf.base_dir = Path('workdir').absolute()
+    return wf
+
+
+if __name__ == "__main__":
+    from argparse import ArgumentParser, RawTextHelpFormatter
+
+    parser = ArgumentParser(
+        description="DCAN subcortical MNI alignment",
+        formatter_class=RawTextHelpFormatter,
+    )
+    parser.add_argument(
+        "bold_file",
+        type=Path,
+        help="the input BOLD file",
+    )
+    parser.add_argument(
+        "bold_roi",
+        type=Path,
+        help="segmentations in BOLD space",
+    )
+    parser.add_argument(
+        "bold_atlas_roi",
+        type=Path,
+        help="segmentations in ROI space, unrefined",
+    )
+    parser.add_argument(
+        "atlas_xfm",
+        type=Path,
+        help="transformation of input BOLD file to MNI space",
+    )
+    parser.add_argument(
+        "--tr",
+        type=float,
+        help="BOLD repetition time. If not provided, NIfTI header information is used",
+    )
+    opts = parser.parse_args()
+    init_workflow(
+        opts.bold_file.absolute(),
+        opts.bold_roi.absolute(),
+        opts.bold_atlas_roi.absolute(),
+        opts.atlas_xfm.absolute(),
+        TR=opts.tr,
+    ).run()