Merge pull request #5 from templateflow/enh/add-annot-files

ENH: Add parcellations (FS's annot files)

scripts/get_annot_tsv.py

@@ -0,0 +1,56 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2024 The NiPreps Developers <nipreps@gmail.com>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+from pathlib import Path
+import click
+import numpy as np
+import pandas as pd
+import nibabel as nb
+
+
+@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(
+        reg_ctable.byteswap().newbyteorder(),
+        columns={
+            "red": np.uint8,
+            "green": np.uint8,
+            "blue": np.uint8,
+            "transparency": np.uint8,
+            "index": np.uint32,
+        }
+    )
+    df["name"] = [n.decode() for n in reg_names]
+    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)
+
+if __name__ == '__main__':
+    run()
+

tpl-fsaverage_atlas-Desikan2006_dseg.json

@@ -0,0 +1,26 @@
+{
+  "Authors":
+  [
+    "Desikan RS",
+    "Killiany RJ"
+  ],
+  "Curators":
+  [
+    "Aleman-Gomez Y",
+    "Esteban O"
+  ],
+  "DescriptionEntity":
+  {
+    "original": "Contains the file as converted with `mris_convert` directly from FreeSurfer's distribution",
+    "curated": "The 'original' version after manual correction of errors by Aleman-Gomez Y."
+  },
+  "Identifier": "Desikan2006",
+  "License": "See LICENSE file",
+  "Name": "Desikan-Killiany Atlas distributed by FreeSurfer 7",
+  "Provenance": "Converted with `mris_convert` from `$FREESURFER_HOME/subjects/fsaverage{,3,4,5,6}/label/{l,r}h.aparc.annot`",
+  "ReferencesAndLinks":
+  [
+    "https://doi.org/10.1016/j.neuroimage.2006.01.021",
+    "https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation"
+  ]
+}

tpl-fsaverage_atlas-Destrieux2005_dseg.json

@@ -0,0 +1,25 @@
+{
+  "Authors":
+  [
+    "Destrieux C",
+    "Fischl B",
+    "Dale AM",
+    "Halgren E"
+  ],
+  "Curators":
+  [
+    "Aleman-Gomez Y",
+    "Esteban O"
+  ],
+  "Identifier": "Destrieux2005",
+  "License": "See LICENSE file",
+  "Name": "Destrieux Atlas (2005) distributed by FreeSurfer 7",
+  "DeprecationNote": "This atlas was updated in 2009 and Destrieux2009 SHOULD be used instead",
+  "Provenance": "Converted with `mris_convert` from `$FREESURFER_HOME/subjects/fsaverage{,3,4,5,6}/label/{l,r}h.aparc.a2005s.annot`",
+  "ReferencesAndLinks":
+  [
+    "https://doi.org/10.1016/j.neuroimage.2010.06.010",
+    "https://doi.org/10.1016/S1053-8119(09)71561-7",
+    "https://surfer.nmr.mgh.harvard.edu/fswiki/DestrieuxAtlasChanges"
+  ]
+}

tpl-fsaverage_atlas-Destrieux2009_dseg.json

@@ -0,0 +1,24 @@
+{
+  "Authors":
+  [
+    "Destrieux C",
+    "Fischl B",
+    "Dale AM",
+    "Halgren E"
+  ],
+  "Curators":
+  [
+    "Aleman-Gomez Y",
+    "Esteban O"
+  ],
+  "Identifier": "Destrieux2009",
+  "License": "See LICENSE file",
+  "Name": "Destrieux Atlas (updated 2009) distributed by FreeSurfer 7",
+  "Provenance": "Converted with `mris_convert` from `$FREESURFER_HOME/subjects/fsaverage{,3,4,5,6}/label/{l,r}h.aparc.a2009s.annot`",
+  "ReferencesAndLinks":
+  [
+    "https://doi.org/10.1016/j.neuroimage.2010.06.010",
+    "https://doi.org/10.1016/S1053-8119(09)71561-7",
+    "https://surfer.nmr.mgh.harvard.edu/fswiki/DestrieuxAtlasChanges"
+  ]
+}

tpl-fsaverage_atlas-Lausanne2018_dseg.json

@@ -0,0 +1,21 @@
+{
+  "Authors":
+  [
+    "Aleman-Gomez Y",
+    "Cammoun L",
+    "Hagmann P"
+  ],
+  "Curators":
+  [
+    "Aleman-Gomez Y",
+    "Esteban O"
+  ],
+  "Identifier": "Lausanne2018",
+  "License": "CC-BY-4",
+  "Name": "Lausanne multi-scale cortical parcellation",
+  "Description": "Symmetric version of the original parcellation by (Cammoun et al., 2012)",
+  "ReferencesAndLinks":
+  [
+    "https://doi.org/10.1016/j.jneumeth.2011.09.031"
+  ]
+}

tpl-fsaverage_atlas-Sabuncu2011_dseg.json

@@ -0,0 +1,20 @@
+{
+  "Authors":
+  [
+    "Sabuncu MR"
+  ],
+  "Curators":
+  [
+    "Aleman-Gomez Y",
+    "Esteban O"
+  ],
+  "Identifier": "Sabuncu2011",
+  "License": "See LICENSE file",
+  "Name": "'Cortical Hubs' (CHubs) from the OASIS template, distributed by FreeSurfer 7",
+  "Provenance": "Converted with `mris_convert` from `$FREESURFER_HOME/subjects/fsaverage{,3,4,5,6}/label/{l,r}h.oasis.chubs.annot`",
+  "ReferencesAndLinks":
+  [
+    "https://doi.org/10.1001/archneurol.2011.167",
+    "https://surfer.nmr.mgh.harvard.edu/fswiki/Chubs"
+  ]
+}

tpl-fsaverage_atlas-Schaefer2018_dseg.json

@@ -0,0 +1,21 @@
+{
+  "Authors":
+  [
+    "Schaefer A",
+    "Yeo BT"
+  ],
+  "Curators":
+  [
+    "Aleman-Gomez Y",
+    "Esteban O"
+  ],
+  "Identifier": "Schaefer2018",
+  "License": "See LICENSE file",
+  "Name": "Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity MRI",
+  "Description": "Multi-scale cortical parcellation — ten scales going from 100 to 1000 parcels that are matched with Yeo2011's networks.",
+  "IsDerivedFrom": "Yeo2011",
+  "ReferencesAndLinks":
+  [
+    "https://doi.org/10.1093/cercor/bhx179"
+  ]
+}

tpl-fsaverage_atlas-Yeo2011_dseg.json

@@ -0,0 +1,21 @@
+{
+  "Authors":
+  [
+    "Yeo BT",
+    "Buckner RL"
+  ],
+  "Curators":
+  [
+    "Aleman-Gomez Y",
+    "Esteban O"
+  ],
+  "Identifier": "Yeo2011",
+  "License": "See LICENSE file",
+  "Name": "Cortical Parcellation Estimated by Intrinsic Functional Connectivity, distributed by FreeSurfer 7",
+  "Provenance": "Converted with `mris_convert` from `$FREESURFER_HOME/subjects/fsaverage{,3,4,5,6}/label/{l,r}h.Yeo2011_{,1}7Networks_N1000.annot`",
+  "ReferencesAndLinks":
+  [
+    "https://doi.org/10.1152/jn.00338.2011",
+    "https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011"
+  ]
+}

tpl-fsaverage_atlas-brainnetome_dseg.json

@@ -0,0 +1,18 @@
+{
+  "Authors":
+  [
+    "Fan L"
+  ],
+  "Curators":
+  [
+    "Aleman-Gomez Y",
+    "Esteban O"
+  ],
+  "Identifier": "brainnetome",
+  "License": "The atlas' data and metadata are the property of the Brainnetome Center. The Brainnetome makes this information available to researchers, scientists and others at colleges, universities, not-for-profit foundations and other similar institutions free of charge, subject to proper attribution and an agreement to share alike, for use for non-commercial purposes. Brainetome Center will consider granting a license to individuals and entities that wish to use the information, images and data for commercial purposes. Such requests should be made to Dr. Lingzhong Fan by e-mail:brainnetome.atlas@nlpr.ia.ac.cn",
+  "Name": "Brainnetome cortical parcellation",
+  "ReferencesAndLinks":
+  [
+    "https://doi.org/10.1093/cercor/bhw157"
+  ]
+}

tpl-fsaverage_hemi-L_atlas-Desikan2006_seg-aparc.tsv

@@ -0,0 +1,37 @@
+index	name	color
+1639705	unknown	#190519ff
+2647065	bankssts	#196428ff
+10511485	caudalanteriorcingulate	#7d64a0ff
+6500	caudalmiddlefrontal	#641900ff
+3294840	corpuscallosum	#784632ff
+6558940	cuneus	#dc1464ff
+660700	entorhinal	#dc140aff
+9231540	fusiform	#b4dc8cff
+14433500	inferiorparietal	#dc3cdcff
+7874740	inferiortemporal	#b42878ff
+9180300	isthmuscingulate	#8c148cff
+9182740	lateraloccipital	#141e8cff
+3296035	lateralorbitofrontal	#234b32ff
+9211105	lingual	#e18c8cff
+4924360	medialorbitofrontal	#c8234bff
+3302560	middletemporal	#a06432ff
+3988500	parahippocampal	#14dc3cff
+3988540	paracentral	#3cdc3cff
+9221340	parsopercularis	#dcb48cff
+3302420	parsorbitalis	#146432ff
+1326300	parstriangularis	#dc3c14ff
+3957880	pericalcarine	#78643cff
+1316060	postcentral	#dc1414ff
+14464220	posteriorcingulate	#dcb4dcff
+14423100	precentral	#3c14dcff
+11832480	precuneus	#a08cb4ff
+9180240	rostralanteriorcingulate	#50148cff
+8204875	rostralmiddlefrontal	#4b327dff
+10542100	superiorfrontal	#14dca0ff
+9221140	superiorparietal	#14b48cff
+14474380	superiortemporal	#8cdcdcff
+1351760	supramarginal	#50a014ff
+6553700	frontalpole	#640064ff
+11146310	temporalpole	#4614aaff
+13145750	transversetemporal	#9696c8ff
+2146559	insula	#ffc020ff

tpl-fsaverage_hemi-L_atlas-Destrieux2005_dseg.tsv

@@ -0,0 +1,83 @@
+index	name	color
+0	Unknown	#000000ff
+3289650	Corpus_callosum	#323232ff
+1971380	G_and_S_Insula_ONLY_AVERAGE	#b4141eff
+1644860	G_cingulate-Isthmus	#3c1919ff
+3947545	G_cingulate-Main_part	#193c3cff
+1316020	G_cuneus	#b41414ff
+6558940	G_frontal_inf-Opercular_part	#dc1464ff
+3947660	G_frontal_inf-Orbital_part	#8c3c3cff
+9231540	G_frontal_inf-Triangular_part	#b4dc8cff
+11822220	G_frontal_middle	#8c64b4ff
+9180340	G_frontal_superior	#b4148cff
+9180300	G_frontomarginal	#8c148cff
+657941	G_insular_long	#150a0aff
+9211105	G_insular_short	#e18c8cff
+11811863	G_and_S_occipital_inferior	#173cb4ff
+11812020	G_occipital_middle	#b43cb4ff
+3988500	G_occipital_superior	#14dc3cff
+9180220	G_occipit-temp_lat-Or_fusiform	#3c148cff
+9221340	G_occipit-temp_med-Lingual_part	#dcb48cff
+1336385	G_occipit-temp_med-Parahippocampal_part	#416414ff
+1326300	G_orbital	#dc3c14ff
+3957820	G_paracentral	#3c643cff
+14433300	G_parietal_inferior-Angular_part	#143cdcff
+3957860	G_parietal_inferior-Supramarginal_part	#64643cff
+14464220	G_parietal_superior	#dcb4dcff
+9221140	G_postcentral	#14b48cff
+11832380	G_precentral	#3c8cb4ff
+9180185	G_precuneus	#19148cff
+6568980	G_rectus	#143c64ff
+1367100	G_subcallosal	#3cdc14ff
+14423100	G_subcentral	#3c14dcff
+6610140	G_temporal_inferior	#dcdc64ff
+3947700	G_temporal_middle	#b43c3cff
+14433340	G_temp_sup-G_temp_transv_and_interm_S	#3c3cdcff
+14433500	G_temp_sup-Lateral_aspect	#dc3cdcff
+3988545	G_temp_sup-Planum_polare	#41dc3cff
+1346585	G_temp_sup-Planum_tempolare	#198c14ff
+16384013	G_and_S_transverse_frontopolar	#0d00faff
+14423101	Lat_Fissure-ant_sgt-ramus_horizontal	#3d14dcff
+3937341	Lat_Fissure-ant_sgt-ramus_vertical	#3d143cff
+6569021	Lat_Fissure-post_sgt	#3d3c64ff
+1644825	Medial_wall	#191919ff
+3937420	Pole_occipital	#8c143cff
+1357020	Pole_temporal	#dcb414ff
+11842623	S_calcarine	#3fb4b4ff
+660701	S_central	#dd140aff
+1367061	S_central_insula	#15dc14ff
+1336503	S_cingulate-Main_part_and_Intracingulate	#b76414ff
+6558941	S_cingulate-Marginalis_part	#dd1464ff
+9190621	S_circular_insula_anterior	#dd3c8cff
+14423261	S_circular_insula_inferior	#dd14dcff
+14474301	S_circular_insula_superior	#3ddcdcff
+13158500	S_collateral_transverse_ant	#64c8c8ff
+13158410	S_collateral_transverse_post	#0ac8c8ff
+1367261	S_frontal_inferior	#dddc14ff
+6558861	S_frontal_middle	#8d1464ff
+6609981	S_frontal_superior	#3ddc64ff
+3988501	S_frontomarginal	#15dc3cff
+1326221	S_intermedius_primus-Jensen	#8d3c14ff
+14423183	S_intraparietal-and_Parietal_transverse	#8f14dcff
+11801661	S_occipital_anterior	#3d14b4ff
+14433381	S_occipital_middle_and_Lunatus	#653cdcff
+9180181	S_occipital_superior_and_transversalis	#15148cff
+1346781	S_occipito-temporal_lateral	#dd8c14ff
+14443661	S_occipito-temporal_medial_and_S_Lingual	#8d64dcff
+1315941	S_orbital-H_shapped	#651414ff
+1336541	S_orbital_lateral	#dd6414ff
+1362101	S_orbital_medial-Or_olfactory	#b5c814ff
+9221141	S_paracentral	#15b48cff
+11822181	S_parieto_occipital	#6564b4ff
+1367221	S_pericallosal	#b5dc14ff
+13143061	S_postcentral	#158cc8ff
+15733781	S_precentral-Inferior-part	#1514f0ff
+13112341	S_precentral-Superior-part	#1514c8ff
+3978301	S_subcentral_ant	#3db43cff
+16430141	S_subcentral_post	#3db4faff
+3937301	S_suborbital	#15143cff
+3947621	S_subparietal	#653c3cff
+14474261	S_supracingulate	#15dcdcff
+11842581	S_temporal_inferior	#15b4b4ff
+3988703	S_temporal_superior	#dfdc3cff
+3947741	S_temporal_transverse	#dd3c3cff