Removed deprecated structures

Author: kdiers

brainprint/asymmetry.py

@@ -28,25 +28,10 @@ def compute_asymmetry(
     Dict[str, float]
         {left_label}_{right_label}, distance.
     """
-    # Define structures
-
-    # combined and individual aseg labels:
-    # - Left  Striatum: left  Caudate + Putamen + Accumbens
-    # - Right Striatum: right Caudate + Putamen + Accumbens
-    # - CorpusCallosum: 5 subregions combined
-    # - Cerebellum: brainstem + (left+right) cerebellum WM and GM
-    # - Ventricles: (left+right) lat.vent + inf.lat.vent + choroidplexus + 3rdVent + CSF
-    # - Lateral-Ventricle: lat.vent + inf.lat.vent + choroidplexus
-    # - 3rd-Ventricle: 3rd-Ventricle + CSF
 
     structures_left_right = [
-        ("Left-Striatum", "Right-Striatum"),
         ("Left-Lateral-Ventricle", "Right-Lateral-Ventricle"),
-        (
-            "Left-Cerebellum-White-Matter",
-            "Right-Cerebellum-White-Matter",
-        ),
-        ("Left-Cerebellum-Cortex", "Right-Cerebellum-Cortex"),
+        ("Left-Cerebellum", "Right-Cerebellum"),
         ("Left-Thalamus-Proper", "Right-Thalamus-Proper"),
         ("Left-Caudate", "Right-Caudate"),
         ("Left-Putamen", "Right-Putamen"),

brainprint/cli/help_text.py

@@ -47,14 +47,11 @@
 
 CorpusCallosum                  [251, 252, 253, 254, 255]
 Cerebellum                      [7, 8, 16, 46, 47]
-Ventricles                      [4, 5, 14, 24, 31, 43, 44, 63]
 3rd-Ventricle                   [14, 24]
 4th-Ventricle                   15
 Brain-Stem                      16
-Left-Striatum                   [11, 12, 26]
 Left-Lateral-Ventricle          [4, 5, 31]
-Left-Cerebellum-White-Matter    7
-Left-Cerebellum-Cortex          8
+Left-Cerebellum                 [7, 8]
 Left-Thalamus-Proper            10
 Left-Caudate                    11
 Left-Putamen                    12
@@ -63,10 +60,8 @@
 Left-Amygdala                   18
 Left-Accumbens-area             26
 Left-VentralDC                  28
-Right-Striatum                  [50, 51, 58]
 Right-Lateral-Ventricle         [43, 44, 63]
-Right-Cerebellum-White-Matter   46
-Right-Cerebellum-Cortex         47
+Right-Cerebellum                [46, 47]
 Right-Thalamus-Proper           49
 Right-Caudate                   50
 Right-Putamen                   51

brainprint/utils/tests/test_files.py

@@ -27,11 +27,8 @@ def test_files_exist_in_directory(sample_subjects_dir, sample_subject_id):
     surface_directory = os.path.join(output_directory, "surfaces")
     surface_files = [
         "aseg.final.10.vtk",
-        "aseg.final.47.vtk",
-        "aseg.final.11_12_26.vtk",
         "aseg.final.49.vtk",
         "aseg.final.11.vtk",
-        "aseg.final.50_51_58.vtk",
         "aseg.final.12.vtk",
         "aseg.final.50.vtk",
         "aseg.final.13.vtk",
@@ -49,16 +46,14 @@ def test_files_exist_in_directory(sample_subjects_dir, sample_subject_id):
         "aseg.final.251_252_253_254_255.vtk",
         "aseg.final.7_8_16_46_47.vtk",
         "aseg.final.26.vtk",
-        "aseg.final.7.vtk",
+        "aseg.final.7_8.vtk",
         "aseg.final.28.vtk",
-        "aseg.final.8.vtk",
         "aseg.final.43_44_63.vtk",
         "lh.pial.vtk",
-        "aseg.final.4_5_14_24_31_43_44_63.vtk",
         "lh.white.vtk",
         "aseg.final.4_5_31.vtk",
         "rh.pial.vtk",
-        "aseg.final.46.vtk",
+        "aseg.final.46_47.vtk",
         "rh.white.vtk",
     ]