Add BEP038-compliant atlas examples of commonly used publicly available atlases

atlas-AAL/atlas-AAL_description.json

@@ -0,0 +1,38 @@
+{
+    "Name": "Automated Anatomical Labeling Atlas 3 - SPM12, version 3v2",
+    "Description": "AAL3v2 atlas for SPM 12. Notes: This atlas is the result of an automated anatomical parcellation of the spatially normalized single-subject high-resolution T1 volume provided by the Montreal Neurological Institute (MNI) (D. L. Collins et al., 1998, Trans. Med. Imag. 17, 463-468, PubMed). Using this parcellation method, three procedures to perform the automated anatomical labeling of functional studies are proposed: (1) labeling of an extremum defined by a set of coordinates, (2) percentage of voxels belonging to each of the AVOI intersected by a sphere centered by a set of coordinates, and (3) percentage of voxels belonging to each of the AVOI intersected by an activated cluster.",
+    "BIDSVersion": "1.11.0",
+    "Authors": [
+        "Edmund T. Rolls",
+        "Chu-Chung Huang",
+        "Ching-Po Lin",
+        "Jianfeng Feng",
+        "Marc Joliot",
+        "Nathalie Tzourio-Mazoyer",
+        "Bernard Landeau",
+        "Dimitri Papathanassiou",
+        "Fabrice Crivello",
+        "Olivier Etard",
+        "Nicolas Delcroix",
+        "Bernard Mazoyer"
+    ],
+    "HowToAcknowledge": "Please cite: (1) Rolls ET, Huang CC, Lin CP, Feng J, Joliot M. Automated anatomical labelling atlas 3. Neuroimage. 2020 Feb 1;206:116189. (2) Tzourio-Mazoyer N, Landeau B, Papathanassiou D, Crivello F, Etard O, Delcroix N, Mazoyer B, Joliot M. Automated anatomical labeling of activations in SPM using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. NeuroImage. 2002;15(1):273-89.",
+    "SourceDatasetsURLs": [
+        "http://www.gin.cnrs.fr/en/tools/aal/",
+        "https://www.oxcns.org/aal3.html"
+    ],
+    "License": "GNU General Public License",
+    "Funding": [
+        "Science and Technology Innovation Plan (No. 15JC1400101 and No. 16JC1420402)"
+    ],
+    "ReferencesAndLinks": [
+        "http://www.gin.cnrs.fr/AAL-217?lang",
+        "https://doi.org/10.1016/j.neuroimage.2019.116189",
+        "https://doi.org/10.1006/nimg.2001.0978",
+        "https://doi.org/10.1016/j.neuroimage.2015.07.075"
+    ],
+    "Species": "Human",
+    "DerivedFrom": "MNI single-subject T1-weighted high-resolution volume (Collins brain)",
+    "SampleSize": 1,
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNIColin27_res-1_T1w.nii.gz"
+}

atlas-AAL/dataset_description.json

@@ -0,0 +1,39 @@
+{
+    "Authors": [
+        "Edmund T. Rolls",
+        "Chu-Chung Huang",
+        "Ching-Po Lin",
+        "Jianfeng Feng",
+        "Marc Joliot",
+        "Nathalie Tzourio-Mazoyer",
+        "Bernard Landeau",
+        "Dimitri Papathanassiou",
+        "Fabrice Crivello",
+        "Olivier Etard",
+        "Nicolas Delcroix",
+        "Bernard Mazoyer"
+    ],
+    "BIDSVersion": "1.11.0",
+    "DatasetType": "derivative",
+    "GeneratedBy": [
+        {
+            "Name": "bids-atlas",
+            "Version": "0.3.1",
+            "CodeURL": "https://github.com/PeerHerholz/bids_atlas"
+        },
+        {
+            "Name": "nilearn",
+            "CodeURL": "https://nilearn.github.io/stable/modules/generated/nilearn.datasets.fetch_atlas_aal.html"
+        }
+    ],
+    "License": "GNU General Public License",
+    "Name": "Automated Anatomical Labeling Atlas 3 - SPM12, version 3v2",
+    "SourceDatasets": [
+        {
+            "URL": "http://www.gin.cnrs.fr/en/tools/aal/"
+        },
+        {
+            "URL": "https://www.oxcns.org/aal3.html"
+        }
+    ]
+}

atlas-AAL/tpl-MNIColin27/anat/tpl-MNIColin27_atlas-AAL_res-1_dseg.json

@@ -0,0 +1,11 @@
+{
+    "Resolution": "1mm isotropic",
+    "hemisphere": {
+        "Description": "Hemisphere location of the region",
+        "Levels": {
+            "L": "Left hemisphere",
+            "R": "Right hemisphere",
+            "n/a": "Not applicable or bilateral"
+        }
+    }
+}

atlas-AAL/tpl-MNIColin27/anat/tpl-MNIColin27_atlas-AAL_res-1_dseg.tsv

@@ -0,0 +1,118 @@
+index	name	hemisphere
+0	Background	n/a
+2001	Precentral_L	L
+2002	Precentral_R	R
+2101	Frontal_Sup_L	L
+2102	Frontal_Sup_R	R
+2111	Frontal_Sup_Orb_L	L
+2112	Frontal_Sup_Orb_R	R
+2201	Frontal_Mid_L	L
+2202	Frontal_Mid_R	R
+2211	Frontal_Mid_Orb_L	L
+2212	Frontal_Mid_Orb_R	R
+2301	Frontal_Inf_Oper_L	L
+2302	Frontal_Inf_Oper_R	R
+2311	Frontal_Inf_Tri_L	L
+2312	Frontal_Inf_Tri_R	R
+2321	Frontal_Inf_Orb_L	L
+2322	Frontal_Inf_Orb_R	R
+2331	Rolandic_Oper_L	L
+2332	Rolandic_Oper_R	R
+2401	Supp_Motor_Area_L	L
+2402	Supp_Motor_Area_R	R
+2501	Olfactory_L	L
+2502	Olfactory_R	R
+2601	Frontal_Sup_Medial_L	L
+2602	Frontal_Sup_Medial_R	R
+2611	Frontal_Med_Orb_L	L
+2612	Frontal_Med_Orb_R	R
+2701	Rectus_L	L
+2702	Rectus_R	R
+3001	Insula_L	L
+3002	Insula_R	R
+4001	Cingulum_Ant_L	L
+4002	Cingulum_Ant_R	R
+4011	Cingulum_Mid_L	L
+4012	Cingulum_Mid_R	R
+4021	Cingulum_Post_L	L
+4022	Cingulum_Post_R	R
+4101	Hippocampus_L	L
+4102	Hippocampus_R	R
+4111	ParaHippocampal_L	L
+4112	ParaHippocampal_R	R
+4201	Amygdala_L	L
+4202	Amygdala_R	R
+5001	Calcarine_L	L
+5002	Calcarine_R	R
+5011	Cuneus_L	L
+5012	Cuneus_R	R
+5021	Lingual_L	L
+5022	Lingual_R	R
+5101	Occipital_Sup_L	L
+5102	Occipital_Sup_R	R
+5201	Occipital_Mid_L	L
+5202	Occipital_Mid_R	R
+5301	Occipital_Inf_L	L
+5302	Occipital_Inf_R	R
+5401	Fusiform_L	L
+5402	Fusiform_R	R
+6001	Postcentral_L	L
+6002	Postcentral_R	R
+6101	Parietal_Sup_L	L
+6102	Parietal_Sup_R	R
+6201	Parietal_Inf_L	L
+6202	Parietal_Inf_R	R
+6211	SupraMarginal_L	L
+6212	SupraMarginal_R	R
+6221	Angular_L	L
+6222	Angular_R	R
+6301	Precuneus_L	L
+6302	Precuneus_R	R
+6401	Paracentral_Lobule_L	L
+6402	Paracentral_Lobule_R	L
+7001	Caudate_L	L
+7002	Caudate_R	R
+7011	Putamen_L	L
+7012	Putamen_R	R
+7021	Pallidum_L	L
+7022	Pallidum_R	R
+7101	Thalamus_L	L
+7102	Thalamus_R	R
+8101	Heschl_L	L
+8102	Heschl_R	R
+8111	Temporal_Sup_L	L
+8112	Temporal_Sup_R	R
+8121	Temporal_Pole_Sup_L	L
+8122	Temporal_Pole_Sup_R	R
+8201	Temporal_Mid_L	L
+8202	Temporal_Mid_R	R
+8211	Temporal_Pole_Mid_L	L
+8212	Temporal_Pole_Mid_R	R
+8301	Temporal_Inf_L	L
+8302	Temporal_Inf_R	R
+9001	Cerebelum_Crus1_L	L
+9002	Cerebelum_Crus1_R	R
+9011	Cerebelum_Crus2_L	L
+9012	Cerebelum_Crus2_R	R
+9021	Cerebelum_3_L	L
+9022	Cerebelum_3_R	R
+9031	Cerebelum_4_5_L	L
+9032	Cerebelum_4_5_R	R
+9041	Cerebelum_6_L	L
+9042	Cerebelum_6_R	R
+9051	Cerebelum_7b_L	L
+9052	Cerebelum_7b_R	R
+9061	Cerebelum_8_L	L
+9062	Cerebelum_8_R	R
+9071	Cerebelum_9_L	L
+9072	Cerebelum_9_R	R
+9081	Cerebelum_10_L	L
+9082	Cerebelum_10_R	R
+9100	Vermis_1_2	n/a
+9110	Vermis_3	n/a
+9120	Vermis_4_5	n/a
+9130	Vermis_6	n/a
+9140	Vermis_7	n/a
+9150	Vermis_8	n/a
+9160	Vermis_9	n/a
+9170	Vermis_10	n/a

atlas-AAL/tpl-MNIColin27/anat/tpl-MNIColin27_res-1_T1w.json

@@ -0,0 +1,22 @@
+{
+    "Authors": [
+        "Holmes CJ",
+        "Hoge R",
+        "Collins DL",
+        "Woods R",
+        "Toga AW",
+        "Evans AC"
+    ],
+    "Curators": [
+        "Esteban O"
+    ],
+    "License": "Copyright (C) 1993\u20132009 Louis Collins, McConnell Brain Imaging Centre,\n                        Montreal Neurological Institute, McGill University.\n\nPermission to use, copy, modify, and distribute this software and its\ndocumentation for any purpose and without fee is hereby granted,\nprovided that the above copyright notice appear in all copies.\nThe authors and McGill University make no representations about the\nsuitability of this software for any purpose.\nIt is provided \"as is\" without express or implied warranty.\nThe authors are not responsible for any data loss, equipment damage,\nproperty loss, or injury to subjects or patients resulting from the\nuse or misuse of this software package.",
+    "Name": "Colin 27 Average Brain, Stereotaxic Registration Model",
+    "ReferencesAndLinks": [
+        "https://doi.org/10.1097/00004728-199803000-00032",
+        "https://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27"
+    ],
+    "Species": "Human",
+    "Resolution": "1mm isotropic",
+    "SkullStripped": false
+}

atlas-Destrieux/atlas-Destrieux_description.json

@@ -0,0 +1,34 @@
+{
+    "Name": "Destrieux cortical deterministic atlas - 2009 version",
+    "Description": "Destrieux cortical atlas is based on a parcellation scheme that first divided the cortex into gyral and sulcal regions, the limit between both being given by the curvature value of the surface. A gyrus only includes the cortex visible on the pial view, the hidden cortex (banks of sulci) are marked sulcus. The result is a complete labeling of cortical sulci and gyri with 74 anatomical parcellations per hemisphere based on standard internationally-accepted nomenclature.",
+    "BIDSVersion": "1.11.0",
+    "Curators": [
+        "Christophe Destrieux",
+        "Bruce Fischl",
+        "Anders Dale",
+        "Eric Halgren"
+    ],
+    "HowToAcknowledge": "Please cite: Destrieux C, Fischl B, Dale A, Halgren E. Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. NeuroImage. 2010;53(1):1-15. doi:10.1016/j.neuroimage.2010.06.010. Also cite: Fischl B, van der Kouwe A, Destrieux C, et al. Automatically Parcellating the Human Cerebral Cortex. Cereb Cortex. 2004;14(1):11-22. doi:10.1093/cercor/bhg087",
+    "SourceDatasetsURLs": [
+        "https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation"
+    ],
+    "License": "FreeSurfer Software License (MGH - royalty-free, non-exclusive, requires registration)",
+    "Funding": [
+        "National Institute for Neurological Disorders and Stroke (R01 NS18741, R01 NS052585)",
+        "National Center for Research Resources (P41-RR14075, NCRR BIRN002, U24 RR021382)",
+        "National Institute for Biomedical Imaging and Bioengineering (R01 EB001550, R01 EB006758, R01 EB009282)",
+        "National Institute on Aging (R01 AG02238)",
+        "Mental Illness and Neuroscience Discovery (MIND) Institute",
+        "National Alliance for Medical Image Computing (NAMIC, U54 EB005149)",
+        "The Autism & Dyslexia Project funded by the Ellison Medical Foundation",
+        "Centre Hospitalier R\u00e9gional et Universitaire de Tours, Tours, France"
+    ],
+    "ReferencesAndLinks": [
+        "https://doi.org/10.1093/cercor/bhg087",
+        "https://doi.org/10.1016/j.neuroimage.2010.06.010"
+    ],
+    "Species": "Human",
+    "DerivedFrom": "Training set of 12 healthy subjects (24 hemispheres) with high-resolution T1-weighted MPRAGE scans (1.5T Siemens Sonata)",
+    "SampleSize": 12,
+    "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-fsaverage_res-1_T1w.nii.gz"
+}

atlas-Destrieux/dataset_description.json

@@ -0,0 +1,25 @@
+{
+    "Authors": [
+        "Unknown"
+    ],
+    "BIDSVersion": "1.11.0",
+    "DatasetType": "derivative",
+    "GeneratedBy": [
+        {
+            "Name": "bids-atlas",
+            "Version": "0.3.1",
+            "CodeURL": "https://github.com/PeerHerholz/bids_atlas"
+        },
+        {
+            "Name": "nilearn",
+            "CodeURL": "https://nilearn.github.io/stable/modules/generated/nilearn.datasets.fetch_atlas_destrieux_2009.html"
+        }
+    ],
+    "License": "FreeSurfer Software License (MGH - royalty-free, non-exclusive, requires registration)",
+    "Name": "Destrieux cortical deterministic atlas - 2009 version",
+    "SourceDatasets": [
+        {
+            "URL": "https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation"
+        }
+    ]
+}

atlas-Destrieux/tpl-fsaverage/anat/tpl-fsaverage_atlas-Destrieux_res-1_dseg.json

@@ -0,0 +1,11 @@
+{
+    "Resolution": "1mm isotropic",
+    "hemisphere": {
+        "Description": "Hemisphere location of the region",
+        "Levels": {
+            "L": "Left hemisphere",
+            "R": "Right hemisphere",
+            "n/a": "Not applicable or bilateral"
+        }
+    }
+}

atlas-Destrieux/tpl-fsaverage/anat/tpl-fsaverage_atlas-Destrieux_res-1_dseg.tsv

@@ -0,0 +1,77 @@
+index	name	hemisphere
+0	Unknown	n/a
+1	G_and_S_frontomargin	n/a
+2	G_and_S_occipital_inf	n/a
+3	G_and_S_paracentral	n/a
+4	G_and_S_subcentral	n/a
+5	G_and_S_transv_frontopol	n/a
+6	G_and_S_cingul-Ant	n/a
+7	G_and_S_cingul-Mid-Ant	n/a
+8	G_and_S_cingul-Mid-Post	n/a
+9	G_cingul-Post-dorsal	n/a
+10	G_cingul-Post-ventral	n/a
+11	G_cuneus	n/a
+12	G_front_inf-Opercular	n/a
+13	G_front_inf-Orbital	n/a
+14	G_front_inf-Triangul	n/a
+15	G_front_middle	n/a
+16	G_front_sup	n/a
+17	G_Ins_lg_and_S_cent_ins	n/a
+18	G_insular_short	n/a
+19	G_occipital_middle	n/a
+20	G_occipital_sup	n/a
+21	G_oc-temp_lat-fusifor	n/a
+22	G_oc-temp_med-Lingual	n/a
+23	G_oc-temp_med-Parahip	n/a
+24	G_orbital	n/a
+25	G_pariet_inf-Angular	n/a
+26	G_pariet_inf-Supramar	n/a
+27	G_parietal_sup	n/a
+28	G_postcentral	n/a
+29	G_precentral	n/a
+30	G_precuneus	n/a
+31	G_rectus	n/a
+32	G_subcallosal	n/a
+33	G_temp_sup-G_T_transv	n/a
+34	G_temp_sup-Lateral	n/a
+35	G_temp_sup-Plan_polar	n/a
+36	G_temp_sup-Plan_tempo	n/a
+37	G_temporal_inf	n/a
+38	G_temporal_middle	n/a
+39	Lat_Fis-ant-Horizont	n/a
+40	Lat_Fis-ant-Vertical	n/a
+41	Lat_Fis-post	n/a
+42	Medial_wall	n/a
+43	Pole_occipital	n/a
+44	Pole_temporal	n/a
+45	S_calcarine	n/a
+46	S_central	n/a
+47	S_cingul-Marginalis	n/a
+48	S_circular_insula_ant	n/a
+49	S_circular_insula_inf	n/a
+50	S_circular_insula_sup	n/a
+51	S_collat_transv_ant	n/a
+52	S_collat_transv_post	n/a
+53	S_front_inf	n/a
+54	S_front_middle	n/a
+55	S_front_sup	n/a
+56	S_interm_prim-Jensen	n/a
+57	S_intrapariet_and_P_trans	n/a
+58	S_oc_middle_and_Lunatus	n/a
+59	S_oc_sup_and_transversal	n/a
+60	S_occipital_ant	n/a
+61	S_oc-temp_lat	n/a
+62	S_oc-temp_med_and_Lingual	n/a
+63	S_orbital_lateral	n/a
+64	S_orbital_med-olfact	n/a
+65	S_orbital-H_Shaped	n/a
+66	S_parieto_occipital	n/a
+67	S_pericallosal	n/a
+68	S_postcentral	n/a
+69	S_precentral-inf-part	n/a
+70	S_precentral-sup-part	n/a
+71	S_suborbital	n/a
+72	S_subparietal	n/a
+73	S_temporal_inf	n/a
+74	S_temporal_sup	n/a
+75	S_temporal_transverse	n/a