ENH: Add script/command to test mcribs

Author: mgxd

nibabies/cli/mcribs.py

@@ -0,0 +1,107 @@
+import os
+from argparse import ArgumentParser
+
+import nipype.pipeline.engine as pe
+from niworkflows.interfaces.nibabel import MapLabels
+
+from nibabies.interfaces.mcribs import MCRIBReconAll
+
+
+def _parser():
+    parser = ArgumentParser(description="Test script for MCRIBS surfaces")
+    parser.add_argument('subject', help='Subject ID')
+    parser.add_argument('t2w', type=os.path.abspath, help='Input T2w (radioisotropic)')
+    parser.add_argument(
+        'segmentation', type=os.path.abspath, help='Input anatomical segmentation in T2w space'
+    )
+    parser.add_argument(
+        '--outdir', type=os.path.abspath, help='Output directory to persist MCRIBS output'
+    )
+    parser.add_argument('--nthreads', type=int, help='Number of threads to parallelize tasks')
+    return parser
+
+
+def main(argv: list = None):
+    pargs = _parser().parse_args(argv)
+
+    t2w_file = _check_file(pargs.t2w)
+    seg_file = _check_file(pargs.segmentation)
+
+    aseg2mcrib = {
+        2: 51,
+        3: 21,
+        4: 49,
+        5: 0,
+        7: 17,
+        8: 17,
+        10: 43,
+        11: 41,
+        12: 47,
+        13: 47,
+        14: 0,
+        15: 0,
+        16: 19,
+        17: 1,
+        18: 3,
+        26: 41,
+        28: 45,
+        31: 49,
+        41: 52,
+        42: 20,
+        43: 50,
+        44: 0,
+        46: 18,
+        47: 18,
+        49: 42,
+        50: 40,
+        51: 46,
+        52: 46,
+        53: 2,
+        54: 4,
+        58: 40,
+        60: 44,
+        63: 50,
+        253: 48,
+    }
+    map_labels = pe.Node(MapLabels(in_file=seg_file, mappings=aseg2mcrib), name='map_labels')
+
+    recon = pe.Node(
+        MCRIBReconAll(subject_id=pargs.subject, t2w_file=t2w_file), name='mcribs_recon'
+    )
+    if pargs.outdir:
+        recon.inputs.outdir = pargs.outdir
+    if pargs.nthreads:
+        recon.inputs.nthreads = pargs.nthreads
+
+    wf = pe.Workflow(f'MRA_{pargs.subject}')
+    wf.connect(map_labels, 'out_file', recon, 'segmentation_file')
+    wf.run()
+
+
+def _check_file(fl: str) -> str:
+    import nibabel as nb
+    import numpy as np
+
+    img = nb.load(fl)
+    if len(img.shape) != 3:
+        raise ValueError('Image {fl} is not 3 dimensional.')
+
+    voxdims = img.header['pixdim'][1:4]
+    if not np.allclose(voxdims, voxdims[1]):
+        raise ValueError(f'Image {fl} is not isotropic: {voxdims}.')
+
+    ornt = nb.io_orientation(img.affine)
+    axcodes = nb.orientations.ornt2axcodes(ornt)
+    if ''.join(axcodes) != 'LAS':
+        las = nb.orientations.axcodes2ornt('LAS')
+        transform = nb.orientations.ornt_transform(ornt, las)
+        reornt = img.as_reoriented(transform)
+        outfl = os.path.abspath(f'LASornt_{os.path.basename(fl)}')
+        print(f'Creating reorientated image {outfl}')
+        reornt.to_filename(outfl)
+        return outfl
+    return fl
+
+
+if __name__ == '__main__':
+    main()

pyproject.toml

@@ -77,6 +77,7 @@ all = ["nibabies[dev,doc,maint,telemetry,test]"]
 
 [project.scripts]
 nibabies = "nibabies.cli.run:main"
+nibabies-mcribs = "nibabies.cli.mcribs:main"
 
 [tool.hatch.metadata]
 allow-direct-references = true