Merge pull request #8 from templateflow/fix/harmonize-tsv-files

FIX: Normalize/harmonize ``*_dseg.tsv`` files corresponding to ``*_dseg.label.gii``
templateflow · Mar 26, 2024 · 8e53ba4 · 8e53ba4
2 parents d12fbb6 + 3d46ed2
commit 8e53ba4
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Showing 127 changed files with 19,188 additions and 19,177 deletions.
diff --git a/scripts/get_annot_tsv.py b/scripts/get_annot_tsv.py
@@ -21,16 +21,32 @@
 #     https://www.nipreps.org/community/licensing/
 #
 from pathlib import Path
+import re
 import click
 import numpy as np
 import pandas as pd
 import nibabel as nb
 
+FREESURFER_DEFAULT_ANNOT_MAPPING = {
+    "lh.aparc.annot": 1000,
+    "rh.aparc.annot": 2000,
+    "lh.aparc.a2005s.annot": 1100,
+    "rh.aparc.a2005s.annot": 2100,
+    "lh.aparc.a2009s.annot": 11100,
+    "rh.aparc.a2009s.annot": 12100,
+}
+
+
+def annot2tsv(input_annot, hemi=None, encoding="utf-8"):
+    input_annot = Path(input_annot)
+
+    hemi = hemi[:2].lower() if hemi is not None else None
+    if hemi not in ('lh', 'rh'):
+        if (hemi_match := re.search(r'([lr]h)\.', input_annot.name)) is not None:
+            hemi = hemi_match.group()[:2].lower()
+        else:
+            raise RuntimeError('Hemisphere could not be determined')
 
-@click.command()
-@click.argument("input_annot", type=click.Path(exists=True))
-@click.argument("output_tsv", type=click.Path())
-def run(input_annot, output_tsv):
     vert_lab, reg_ctable, reg_names = nb.freesurfer.read_annot(input_annot)
 
     df = pd.DataFrame(
@@ -43,14 +59,51 @@ def run(input_annot, output_tsv):
             "index": np.uint32,
         }
     )
-    df["name"] = [n.decode() for n in reg_names]
+
+    df["hemi"] = hemi[0].upper()
     df["alpha"] = 255 - df.transparency
     df["color"] = df.loc[:, ("red", "green", "blue", "alpha")].apply(
         lambda r: "#{:02x}{:02x}{:02x}{:02x}".format(*r),
         axis=1
     )
-    df[["index", "name", "color"]].to_csv(output_tsv, sep="\t", index=None)
+    df["name"] = [n.decode(encoding) for n in reg_names]
+
+    retcols = ["index", "hemi", "name", "color"]
+    if (
+        offset := FREESURFER_DEFAULT_ANNOT_MAPPING.get(input_annot.name, None)
+    ) is not None:
+        df["fs_index"] = np.arange(len(df), dtype=np.uint32) + offset
+
+        sep = "_" if input_annot.name.endswith("a2009s.annot") else "-"
+        df["fs_name"] = [sep.join(('ctx', hemi, n)) for n in df["name"]]
+        retcols += ["fs_index", "fs_name"]
+
+    return df[retcols]
+
+
+@click.command()
+@click.argument("input_annot", type=click.Path(exists=True))
+@click.argument("output_tsv", type=click.Path())
+def run(input_annot, output_tsv, encoding="utf-8"):
+
+    input_annot = Path(input_annot)
+    lh_annot = (
+        input_annot if input_annot.name.startswith('lh')
+        else input_annot.parent / input_annot.name.replace('rh', 'lh')
+    )
+    rh_annot = (
+        input_annot if input_annot.name.startswith('rh')
+        else input_annot.parent / input_annot.name.replace('lh', 'rh')
+    )
+
+    df = pd.concat([
+        annot2tsv(a, encoding=encoding) for a in (lh_annot, rh_annot)
+    ])
+
+    df.to_csv(
+        output_tsv, sep="\t", index=None
+    )
+
 
 if __name__ == '__main__':
     run()
-
diff --git a/tpl-fsaverage_atlas-Desikan2006_dseg.tsv b/tpl-fsaverage_atlas-Desikan2006_dseg.tsv
@@ -0,0 +1,73 @@
+index	hemi	name	color	fs_index	fs_name
+1639705	L	unknown	#190519ff	1000	ctx-lh-unknown
+2647065	L	bankssts	#196428ff	1001	ctx-lh-bankssts
+10511485	L	caudalanteriorcingulate	#7d64a0ff	1002	ctx-lh-caudalanteriorcingulate
+6500	L	caudalmiddlefrontal	#641900ff	1003	ctx-lh-caudalmiddlefrontal
+3294840	L	corpuscallosum	#784632ff	1004	ctx-lh-corpuscallosum
+6558940	L	cuneus	#dc1464ff	1005	ctx-lh-cuneus
+660700	L	entorhinal	#dc140aff	1006	ctx-lh-entorhinal
+9231540	L	fusiform	#b4dc8cff	1007	ctx-lh-fusiform
+14433500	L	inferiorparietal	#dc3cdcff	1008	ctx-lh-inferiorparietal
+7874740	L	inferiortemporal	#b42878ff	1009	ctx-lh-inferiortemporal
+9180300	L	isthmuscingulate	#8c148cff	1010	ctx-lh-isthmuscingulate
+9182740	L	lateraloccipital	#141e8cff	1011	ctx-lh-lateraloccipital
+3296035	L	lateralorbitofrontal	#234b32ff	1012	ctx-lh-lateralorbitofrontal
+9211105	L	lingual	#e18c8cff	1013	ctx-lh-lingual
+4924360	L	medialorbitofrontal	#c8234bff	1014	ctx-lh-medialorbitofrontal
+3302560	L	middletemporal	#a06432ff	1015	ctx-lh-middletemporal
+3988500	L	parahippocampal	#14dc3cff	1016	ctx-lh-parahippocampal
+3988540	L	paracentral	#3cdc3cff	1017	ctx-lh-paracentral
+9221340	L	parsopercularis	#dcb48cff	1018	ctx-lh-parsopercularis
+3302420	L	parsorbitalis	#146432ff	1019	ctx-lh-parsorbitalis
+1326300	L	parstriangularis	#dc3c14ff	1020	ctx-lh-parstriangularis
+3957880	L	pericalcarine	#78643cff	1021	ctx-lh-pericalcarine
+1316060	L	postcentral	#dc1414ff	1022	ctx-lh-postcentral
+14464220	L	posteriorcingulate	#dcb4dcff	1023	ctx-lh-posteriorcingulate
+14423100	L	precentral	#3c14dcff	1024	ctx-lh-precentral
+11832480	L	precuneus	#a08cb4ff	1025	ctx-lh-precuneus
+9180240	L	rostralanteriorcingulate	#50148cff	1026	ctx-lh-rostralanteriorcingulate
+8204875	L	rostralmiddlefrontal	#4b327dff	1027	ctx-lh-rostralmiddlefrontal
+10542100	L	superiorfrontal	#14dca0ff	1028	ctx-lh-superiorfrontal
+9221140	L	superiorparietal	#14b48cff	1029	ctx-lh-superiorparietal
+14474380	L	superiortemporal	#8cdcdcff	1030	ctx-lh-superiortemporal
+1351760	L	supramarginal	#50a014ff	1031	ctx-lh-supramarginal
+6553700	L	frontalpole	#640064ff	1032	ctx-lh-frontalpole
+11146310	L	temporalpole	#4614aaff	1033	ctx-lh-temporalpole
+13145750	L	transversetemporal	#9696c8ff	1034	ctx-lh-transversetemporal
+2146559	L	insula	#ffc020ff	1035	ctx-lh-insula
+1639705	R	unknown	#190519ff	2000	ctx-rh-unknown
+2647065	R	bankssts	#196428ff	2001	ctx-rh-bankssts
+10511485	R	caudalanteriorcingulate	#7d64a0ff	2002	ctx-rh-caudalanteriorcingulate
+6500	R	caudalmiddlefrontal	#641900ff	2003	ctx-rh-caudalmiddlefrontal
+3294840	R	corpuscallosum	#784632ff	2004	ctx-rh-corpuscallosum
+6558940	R	cuneus	#dc1464ff	2005	ctx-rh-cuneus
+660700	R	entorhinal	#dc140aff	2006	ctx-rh-entorhinal
+9231540	R	fusiform	#b4dc8cff	2007	ctx-rh-fusiform
+14433500	R	inferiorparietal	#dc3cdcff	2008	ctx-rh-inferiorparietal
+7874740	R	inferiortemporal	#b42878ff	2009	ctx-rh-inferiortemporal
+9180300	R	isthmuscingulate	#8c148cff	2010	ctx-rh-isthmuscingulate
+9182740	R	lateraloccipital	#141e8cff	2011	ctx-rh-lateraloccipital
+3296035	R	lateralorbitofrontal	#234b32ff	2012	ctx-rh-lateralorbitofrontal
+9211105	R	lingual	#e18c8cff	2013	ctx-rh-lingual
+4924360	R	medialorbitofrontal	#c8234bff	2014	ctx-rh-medialorbitofrontal
+3302560	R	middletemporal	#a06432ff	2015	ctx-rh-middletemporal
+3988500	R	parahippocampal	#14dc3cff	2016	ctx-rh-parahippocampal
+3988540	R	paracentral	#3cdc3cff	2017	ctx-rh-paracentral
+9221340	R	parsopercularis	#dcb48cff	2018	ctx-rh-parsopercularis
+3302420	R	parsorbitalis	#146432ff	2019	ctx-rh-parsorbitalis
+1326300	R	parstriangularis	#dc3c14ff	2020	ctx-rh-parstriangularis
+3957880	R	pericalcarine	#78643cff	2021	ctx-rh-pericalcarine
+1316060	R	postcentral	#dc1414ff	2022	ctx-rh-postcentral
+14464220	R	posteriorcingulate	#dcb4dcff	2023	ctx-rh-posteriorcingulate
+14423100	R	precentral	#3c14dcff	2024	ctx-rh-precentral
+11832480	R	precuneus	#a08cb4ff	2025	ctx-rh-precuneus
+9180240	R	rostralanteriorcingulate	#50148cff	2026	ctx-rh-rostralanteriorcingulate
+8204875	R	rostralmiddlefrontal	#4b327dff	2027	ctx-rh-rostralmiddlefrontal
+10542100	R	superiorfrontal	#14dca0ff	2028	ctx-rh-superiorfrontal
+9221140	R	superiorparietal	#14b48cff	2029	ctx-rh-superiorparietal
+14474380	R	superiortemporal	#8cdcdcff	2030	ctx-rh-superiortemporal
+1351760	R	supramarginal	#50a014ff	2031	ctx-rh-supramarginal
+6553700	R	frontalpole	#640064ff	2032	ctx-rh-frontalpole
+11146310	R	temporalpole	#4614aaff	2033	ctx-rh-temporalpole
+13145750	R	transversetemporal	#9696c8ff	2034	ctx-rh-transversetemporal
+2146559	R	insula	#ffc020ff	2035	ctx-rh-insula
diff --git a/tpl-fsaverage_atlas-Destrieux2005_dseg.tsv b/tpl-fsaverage_atlas-Destrieux2005_dseg.tsv
@@ -0,0 +1,165 @@
+index	hemi	name	color	fs_index	fs_name
+0	L	Unknown	#000000ff	1100	ctx-lh-Unknown
+3289650	L	Corpus_callosum	#323232ff	1101	ctx-lh-Corpus_callosum
+1971380	L	G_and_S_Insula_ONLY_AVERAGE	#b4141eff	1102	ctx-lh-G_and_S_Insula_ONLY_AVERAGE
+1644860	L	G_cingulate-Isthmus	#3c1919ff	1103	ctx-lh-G_cingulate-Isthmus
+3947545	L	G_cingulate-Main_part	#193c3cff	1104	ctx-lh-G_cingulate-Main_part
+1316020	L	G_cuneus	#b41414ff	1105	ctx-lh-G_cuneus
+6558940	L	G_frontal_inf-Opercular_part	#dc1464ff	1106	ctx-lh-G_frontal_inf-Opercular_part
+3947660	L	G_frontal_inf-Orbital_part	#8c3c3cff	1107	ctx-lh-G_frontal_inf-Orbital_part
+9231540	L	G_frontal_inf-Triangular_part	#b4dc8cff	1108	ctx-lh-G_frontal_inf-Triangular_part
+11822220	L	G_frontal_middle	#8c64b4ff	1109	ctx-lh-G_frontal_middle
+9180340	L	G_frontal_superior	#b4148cff	1110	ctx-lh-G_frontal_superior
+9180300	L	G_frontomarginal	#8c148cff	1111	ctx-lh-G_frontomarginal
+657941	L	G_insular_long	#150a0aff	1112	ctx-lh-G_insular_long
+9211105	L	G_insular_short	#e18c8cff	1113	ctx-lh-G_insular_short
+11811863	L	G_and_S_occipital_inferior	#173cb4ff	1114	ctx-lh-G_and_S_occipital_inferior
+11812020	L	G_occipital_middle	#b43cb4ff	1115	ctx-lh-G_occipital_middle
+3988500	L	G_occipital_superior	#14dc3cff	1116	ctx-lh-G_occipital_superior
+9180220	L	G_occipit-temp_lat-Or_fusiform	#3c148cff	1117	ctx-lh-G_occipit-temp_lat-Or_fusiform
+9221340	L	G_occipit-temp_med-Lingual_part	#dcb48cff	1118	ctx-lh-G_occipit-temp_med-Lingual_part
+1336385	L	G_occipit-temp_med-Parahippocampal_part	#416414ff	1119	ctx-lh-G_occipit-temp_med-Parahippocampal_part
+1326300	L	G_orbital	#dc3c14ff	1120	ctx-lh-G_orbital
+3957820	L	G_paracentral	#3c643cff	1121	ctx-lh-G_paracentral
+14433300	L	G_parietal_inferior-Angular_part	#143cdcff	1122	ctx-lh-G_parietal_inferior-Angular_part
+3957860	L	G_parietal_inferior-Supramarginal_part	#64643cff	1123	ctx-lh-G_parietal_inferior-Supramarginal_part
+14464220	L	G_parietal_superior	#dcb4dcff	1124	ctx-lh-G_parietal_superior
+9221140	L	G_postcentral	#14b48cff	1125	ctx-lh-G_postcentral
+11832380	L	G_precentral	#3c8cb4ff	1126	ctx-lh-G_precentral
+9180185	L	G_precuneus	#19148cff	1127	ctx-lh-G_precuneus
+6568980	L	G_rectus	#143c64ff	1128	ctx-lh-G_rectus
+1367100	L	G_subcallosal	#3cdc14ff	1129	ctx-lh-G_subcallosal
+14423100	L	G_subcentral	#3c14dcff	1130	ctx-lh-G_subcentral
+6610140	L	G_temporal_inferior	#dcdc64ff	1131	ctx-lh-G_temporal_inferior
+3947700	L	G_temporal_middle	#b43c3cff	1132	ctx-lh-G_temporal_middle
+14433340	L	G_temp_sup-G_temp_transv_and_interm_S	#3c3cdcff	1133	ctx-lh-G_temp_sup-G_temp_transv_and_interm_S
+14433500	L	G_temp_sup-Lateral_aspect	#dc3cdcff	1134	ctx-lh-G_temp_sup-Lateral_aspect
+3988545	L	G_temp_sup-Planum_polare	#41dc3cff	1135	ctx-lh-G_temp_sup-Planum_polare
+1346585	L	G_temp_sup-Planum_tempolare	#198c14ff	1136	ctx-lh-G_temp_sup-Planum_tempolare
+16384013	L	G_and_S_transverse_frontopolar	#0d00faff	1137	ctx-lh-G_and_S_transverse_frontopolar
+14423101	L	Lat_Fissure-ant_sgt-ramus_horizontal	#3d14dcff	1138	ctx-lh-Lat_Fissure-ant_sgt-ramus_horizontal
+3937341	L	Lat_Fissure-ant_sgt-ramus_vertical	#3d143cff	1139	ctx-lh-Lat_Fissure-ant_sgt-ramus_vertical
+6569021	L	Lat_Fissure-post_sgt	#3d3c64ff	1140	ctx-lh-Lat_Fissure-post_sgt
+1644825	L	Medial_wall	#191919ff	1141	ctx-lh-Medial_wall
+3937420	L	Pole_occipital	#8c143cff	1142	ctx-lh-Pole_occipital
+1357020	L	Pole_temporal	#dcb414ff	1143	ctx-lh-Pole_temporal
+11842623	L	S_calcarine	#3fb4b4ff	1144	ctx-lh-S_calcarine
+660701	L	S_central	#dd140aff	1145	ctx-lh-S_central
+1367061	L	S_central_insula	#15dc14ff	1146	ctx-lh-S_central_insula
+1336503	L	S_cingulate-Main_part_and_Intracingulate	#b76414ff	1147	ctx-lh-S_cingulate-Main_part_and_Intracingulate
+6558941	L	S_cingulate-Marginalis_part	#dd1464ff	1148	ctx-lh-S_cingulate-Marginalis_part
+9190621	L	S_circular_insula_anterior	#dd3c8cff	1149	ctx-lh-S_circular_insula_anterior
+14423261	L	S_circular_insula_inferior	#dd14dcff	1150	ctx-lh-S_circular_insula_inferior
+14474301	L	S_circular_insula_superior	#3ddcdcff	1151	ctx-lh-S_circular_insula_superior
+13158500	L	S_collateral_transverse_ant	#64c8c8ff	1152	ctx-lh-S_collateral_transverse_ant
+13158410	L	S_collateral_transverse_post	#0ac8c8ff	1153	ctx-lh-S_collateral_transverse_post
+1367261	L	S_frontal_inferior	#dddc14ff	1154	ctx-lh-S_frontal_inferior
+6558861	L	S_frontal_middle	#8d1464ff	1155	ctx-lh-S_frontal_middle
+6609981	L	S_frontal_superior	#3ddc64ff	1156	ctx-lh-S_frontal_superior
+3988501	L	S_frontomarginal	#15dc3cff	1157	ctx-lh-S_frontomarginal
+1326221	L	S_intermedius_primus-Jensen	#8d3c14ff	1158	ctx-lh-S_intermedius_primus-Jensen
+14423183	L	S_intraparietal-and_Parietal_transverse	#8f14dcff	1159	ctx-lh-S_intraparietal-and_Parietal_transverse
+11801661	L	S_occipital_anterior	#3d14b4ff	1160	ctx-lh-S_occipital_anterior
+14433381	L	S_occipital_middle_and_Lunatus	#653cdcff	1161	ctx-lh-S_occipital_middle_and_Lunatus
+9180181	L	S_occipital_superior_and_transversalis	#15148cff	1162	ctx-lh-S_occipital_superior_and_transversalis
+1346781	L	S_occipito-temporal_lateral	#dd8c14ff	1163	ctx-lh-S_occipito-temporal_lateral
+14443661	L	S_occipito-temporal_medial_and_S_Lingual	#8d64dcff	1164	ctx-lh-S_occipito-temporal_medial_and_S_Lingual
+1315941	L	S_orbital-H_shapped	#651414ff	1165	ctx-lh-S_orbital-H_shapped
+1336541	L	S_orbital_lateral	#dd6414ff	1166	ctx-lh-S_orbital_lateral
+1362101	L	S_orbital_medial-Or_olfactory	#b5c814ff	1167	ctx-lh-S_orbital_medial-Or_olfactory
+9221141	L	S_paracentral	#15b48cff	1168	ctx-lh-S_paracentral
+11822181	L	S_parieto_occipital	#6564b4ff	1169	ctx-lh-S_parieto_occipital
+1367221	L	S_pericallosal	#b5dc14ff	1170	ctx-lh-S_pericallosal
+13143061	L	S_postcentral	#158cc8ff	1171	ctx-lh-S_postcentral
+15733781	L	S_precentral-Inferior-part	#1514f0ff	1172	ctx-lh-S_precentral-Inferior-part
+13112341	L	S_precentral-Superior-part	#1514c8ff	1173	ctx-lh-S_precentral-Superior-part
+3978301	L	S_subcentral_ant	#3db43cff	1174	ctx-lh-S_subcentral_ant
+16430141	L	S_subcentral_post	#3db4faff	1175	ctx-lh-S_subcentral_post
+3937301	L	S_suborbital	#15143cff	1176	ctx-lh-S_suborbital
+3947621	L	S_subparietal	#653c3cff	1177	ctx-lh-S_subparietal
+14474261	L	S_supracingulate	#15dcdcff	1178	ctx-lh-S_supracingulate
+11842581	L	S_temporal_inferior	#15b4b4ff	1179	ctx-lh-S_temporal_inferior
+3988703	L	S_temporal_superior	#dfdc3cff	1180	ctx-lh-S_temporal_superior
+3947741	L	S_temporal_transverse	#dd3c3cff	1181	ctx-lh-S_temporal_transverse
+0	R	Unknown	#000000ff	2100	ctx-rh-Unknown
+3289650	R	Corpus_callosum	#323232ff	2101	ctx-rh-Corpus_callosum
+1971380	R	G_and_S_Insula_ONLY_AVERAGE	#b4141eff	2102	ctx-rh-G_and_S_Insula_ONLY_AVERAGE
+1644860	R	G_cingulate-Isthmus	#3c1919ff	2103	ctx-rh-G_cingulate-Isthmus
+3947545	R	G_cingulate-Main_part	#193c3cff	2104	ctx-rh-G_cingulate-Main_part
+1316020	R	G_cuneus	#b41414ff	2105	ctx-rh-G_cuneus
+6558940	R	G_frontal_inf-Opercular_part	#dc1464ff	2106	ctx-rh-G_frontal_inf-Opercular_part
+3947660	R	G_frontal_inf-Orbital_part	#8c3c3cff	2107	ctx-rh-G_frontal_inf-Orbital_part
+9231540	R	G_frontal_inf-Triangular_part	#b4dc8cff	2108	ctx-rh-G_frontal_inf-Triangular_part
+11822220	R	G_frontal_middle	#8c64b4ff	2109	ctx-rh-G_frontal_middle
+9180340	R	G_frontal_superior	#b4148cff	2110	ctx-rh-G_frontal_superior
+9180300	R	G_frontomarginal	#8c148cff	2111	ctx-rh-G_frontomarginal
+657941	R	G_insular_long	#150a0aff	2112	ctx-rh-G_insular_long
+9211105	R	G_insular_short	#e18c8cff	2113	ctx-rh-G_insular_short
+11811863	R	G_and_S_occipital_inferior	#173cb4ff	2114	ctx-rh-G_and_S_occipital_inferior
+11812020	R	G_occipital_middle	#b43cb4ff	2115	ctx-rh-G_occipital_middle
+3988500	R	G_occipital_superior	#14dc3cff	2116	ctx-rh-G_occipital_superior
+9180220	R	G_occipit-temp_lat-Or_fusiform	#3c148cff	2117	ctx-rh-G_occipit-temp_lat-Or_fusiform
+9221340	R	G_occipit-temp_med-Lingual_part	#dcb48cff	2118	ctx-rh-G_occipit-temp_med-Lingual_part
+1336385	R	G_occipit-temp_med-Parahippocampal_part	#416414ff	2119	ctx-rh-G_occipit-temp_med-Parahippocampal_part
+1326300	R	G_orbital	#dc3c14ff	2120	ctx-rh-G_orbital
+3957820	R	G_paracentral	#3c643cff	2121	ctx-rh-G_paracentral
+14433300	R	G_parietal_inferior-Angular_part	#143cdcff	2122	ctx-rh-G_parietal_inferior-Angular_part
+3957860	R	G_parietal_inferior-Supramarginal_part	#64643cff	2123	ctx-rh-G_parietal_inferior-Supramarginal_part
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