|
|
@@ -34,7 +34,7 @@ def find_optimal_index(slice_path, template_path, approx, temporary_directory, d
|
|
|
nib.save(nib.Nifti1Image(registered_data, np.eye(4)), registered_loc)
|
|
|
|
|
|
mutualinfo = tools.mutual_info_mask(template_data, registered_data)
|
|
|
- norm_factor = scipy.stats.norm.pdf(i-approx+dist, dist, dist*2) / scipy.stats.norm.pdf(dist, dist, dist*2)
|
|
|
+ norm_factor = scipy.stats.norm.pdf(i-approx+dist, dist, dist*10) / scipy.stats.norm.pdf(dist, dist, dist*10)
|
|
|
dice_coef = tools.dice_coef(template_data, registered_data)
|
|
|
weights.append((i, norm_factor * (0.7 * mutualinfo + 0.3 * dice_coef)))
|
|
|
|
|
|
@@ -47,7 +47,6 @@ def apply_transform(segmentation, fixed, index, out_dir, temporary_directory):
|
|
|
|
|
|
seg_slice_loc = out_dir / "segment_slice.nii"
|
|
|
tools.save_slice(str(segmentation), str(seg_slice_loc), index, np.eye(4), nib.load(str(fixed)).header)
|
|
|
- # post_transform_loc = out_dir / f'{seg_slice_loc.stem}_t.nii'
|
|
|
post_transform_loc = out_dir / f'Segmentation.nii'
|
|
|
|
|
|
template_slice_loc = str(temporary_directory / f't_slice{index}.nii')
|
