fixed for subsegmentation and lapy+cc contour

Author: ClePol

CorpusCallosum/fastsurfer_cc.py

@@ -180,7 +180,7 @@ def _set_help_sid(action):
     )
     parser.add_argument(
         "--contour_smoothing",
-        type=float,
+        type=int,
         default=5,
         help="Gaussian sigma for smoothing during contour detection. Higher values mean a smoother CC outline, at the "
              "cost of precision.",
@@ -877,6 +877,7 @@ def _orig2midslab_vox2vox(additional_context: int = 0) -> AffineMatrix4x4:
 
     # save segmentation labels, this
     if sd.has_attribute("cc_segmentation"):
+        sd.filename_by_attribute("cc_segmentation").parent.mkdir(exist_ok=True, parents=True)
         io_futures.append(thread_executor().submit(
             nib.save,
             nib.MGHImage(cc_fn_seg_labels, fsaverage_midslab_vox2ras, orig.header),
@@ -956,13 +957,15 @@ def _orig2midslab_vox2vox(additional_context: int = 0) -> AffineMatrix4x4:
 
 
     if sd.has_attribute("cc_mid_measures"):
+        sd.filename_by_attribute('cc_mid_measures').parent.mkdir(exist_ok=True, parents=True)
         io_futures.append(thread_executor().submit(
             save_cc_measures_json,
             sd.filename_by_attribute('cc_mid_measures'),
             output_metrics_middle_slice | additional_metrics,
         ))
 
     if sd.has_attribute("cc_measures"):
+        sd.filename_by_attribute("cc_measures").parent.mkdir(exist_ok=True, parents=True)
         io_futures.append(thread_executor().submit(
             save_cc_measures_json,
             sd.filename_by_attribute("cc_measures"),
@@ -972,7 +975,7 @@ def _orig2midslab_vox2vox(additional_context: int = 0) -> AffineMatrix4x4:
     # save lta to fsaverage space
 
     if sd.has_attribute("upright_lta"):
-        sd.filename_by_attribute("cc_mid_measures").parent.mkdir(exist_ok=True, parents=True)
+        sd.filename_by_attribute("upright_lta").parent.mkdir(exist_ok=True, parents=True)
         logger.info(f"Saving LTA to fsaverage space: {sd.filename_by_attribute('upright_lta')}")
         io_futures.append(thread_executor().submit(
             write_lta,

CorpusCallosum/shape/contour.py

@@ -773,10 +773,11 @@ def from_mask_and_acpc(
         _contour: Points2dType = skimage.measure.find_contours(cc_mask, level=0.5)[0]
 
         # FIXME: maybe CCContour should just inherit from Polygon?
+        # remove last, duplicate point
+        _contour = _contour[:-1]
         polygon = lapy.polygon.Polygon(np.concatenate([np.zeros_like(_contour[:, :1]), _contour], axis=1), closed=True)
         polygon.smooth_laplace(n=contour_smoothing, inplace=True)
-        polygon.resample(701, inplace=True)
-
+        polygon.resample(700, inplace=True)
         contour_ras = apply_affine(slice_vox2ras, polygon.points)
 
         ac_pc_3d = np.concatenate([[[0], [0]], np.stack([ac_2d, pc_2d], axis=0)], axis=1) # (2, 3)

CorpusCallosum/shape/postprocessing.py

@@ -581,7 +581,10 @@ def make_subdivision_mask(
     coords_vox = np.stack(np.mgrid[0:1, 0:rows, 0:cols], axis=-1)
     coords_ras = apply_affine(vox2ras, coords_vox)
 
-    cc_labels_posterior_to_anterior = SUBSEGMENT_LABELS
+    # Use only as many labels as needed based on the number of subdivisions
+    # Number of regions = number of division lines + 1
+    num_labels_needed = len(subdivision_segments) + 1
+    cc_labels_posterior_to_anterior = SUBSEGMENT_LABELS[:num_labels_needed]
 
     # Initialize with first segment label
     subdivision_mask = np.full(slice_shape, cc_labels_posterior_to_anterior[0], dtype=np.int32)