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FIX: BundleParc -- min_blob_size and keep_biggest were not used #1287

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FIX: BundleParc -- min_blob_size and keep_biggest were not used #1287

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FIX: min_blob_size and keep_biggest were not used
AntoineTheb Dec 2, 2025
7f1d4e5
Update src/scilpy/cli/scil_fodf_bundleparc.py
AntoineTheb Dec 2, 2025
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19 changes: 13 additions & 6 deletions src/scilpy/cli/scil_fodf_bundleparc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -83,6 +83,9 @@ def _build_arg_parser():
'and weights of model. Default is '
'[%(default)s]. If the file does not exist, it '
'will be downloaded.')
parser.add_argument('--volume_size', default=128, type=int,
help='Size of volume to resample to for inference. '
'Only modify if you know what you are doing. ')
parcel_group = parser.add_mutually_exclusive_group()
parcel_group.add_argument('--nb_pts', type=int, default=10,
help='Number of divisions per bundle. Default is'
Expand Down Expand Up @@ -130,7 +133,7 @@ def main():

# TODO in future release: infer these from model
n_coefs = 45
img_size = 128
img_size = args.volume_size

# Check the number of coefficients in the input fODF
if C < n_coefs:
Expand Down Expand Up @@ -164,12 +167,16 @@ def main():
# Predict label maps. `predict` is a generator
# yielding one label map per bundle and its name.
for y_hat_label, b_name in predict(
model, resampled_img.get_fdata(dtype=np.float32), n_coefs,
label_function, DEFAULT_BUNDLES, args.keep_biggest_blob,
args.half_precision,
logging.getLogger().getEffectiveLevel() < logging.WARNING
model,
resampled_img.get_fdata(dtype=np.float32),
n_coefs,
label_function,
DEFAULT_BUNDLES,
args.min_blob_size,
args.keep_biggest_blob,
half_precision=args.half_precision,
verbose=logging.getLogger().getEffectiveLevel() < logging.WARNING
):

# Format the output as a nifti image
label_img = nib.Nifti1Image(y_hat_label,
resampled_img.affine,
Expand Down