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Merge pull request #518 from PeerHerholz/add-atlas-examples-peer
Add BEP038-compliant atlas examples of commonly used publicly available atlases
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‎atlas-AAL/atlas-AAL_description.json‎

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{
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"Name": "Automated Anatomical Labeling Atlas 3 - SPM12, version 3v2",
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"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.",
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"BIDSVersion": "1.11.0",
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"Authors": [
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"Edmund T. Rolls",
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"Chu-Chung Huang",
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"Ching-Po Lin",
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"Jianfeng Feng",
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"Marc Joliot",
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"Nathalie Tzourio-Mazoyer",
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"Bernard Landeau",
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"Dimitri Papathanassiou",
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"Fabrice Crivello",
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"Olivier Etard",
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"Nicolas Delcroix",
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"Bernard Mazoyer"
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],
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"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.",
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"SourceDatasetsURLs": [
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"http://www.gin.cnrs.fr/en/tools/aal/",
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"https://www.oxcns.org/aal3.html"
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],
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"License": "GNU General Public License",
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"Funding": [
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"Science and Technology Innovation Plan (No. 15JC1400101 and No. 16JC1420402)"
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],
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"ReferencesAndLinks": [
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"http://www.gin.cnrs.fr/AAL-217?lang",
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"https://doi.org/10.1016/j.neuroimage.2019.116189",
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"https://doi.org/10.1006/nimg.2001.0978",
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"https://doi.org/10.1016/j.neuroimage.2015.07.075"
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],
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"Species": "Human",
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"DerivedFrom": "MNI single-subject T1-weighted high-resolution volume (Collins brain)",
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"SampleSize": 1,
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"SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNIColin27_res-1_T1w.nii.gz"
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}

‎atlas-AAL/dataset_description.json‎

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

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

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

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

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

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

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

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{
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"Authors": [
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"Holmes CJ",
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"Hoge R",
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"Collins DL",
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"Woods R",
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"Toga AW",
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"Evans AC"
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],
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"Curators": [
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"Esteban O"
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],
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"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.",
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"Name": "Colin 27 Average Brain, Stereotaxic Registration Model",
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"ReferencesAndLinks": [
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"https://doi.org/10.1097/00004728-199803000-00032",
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"https://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27"
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],
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"Species": "Human",
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"Resolution": "1mm isotropic",
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"SkullStripped": false
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}

‎atlas-AAL/tpl-MNIColin27/anat/tpl-MNIColin27_res-1_T1w.nii.gz‎

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‎atlas-Destrieux/atlas-Destrieux_description.json‎

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{
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"Name": "Destrieux cortical deterministic atlas - 2009 version",
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"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.",
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"BIDSVersion": "1.11.0",
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"Curators": [
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"Christophe Destrieux",
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"Bruce Fischl",
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"Anders Dale",
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"Eric Halgren"
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],
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"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",
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"SourceDatasetsURLs": [
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"https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation"
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],
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"License": "FreeSurfer Software License (MGH - royalty-free, non-exclusive, requires registration)",
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"Funding": [
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"National Institute for Neurological Disorders and Stroke (R01 NS18741, R01 NS052585)",
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"National Center for Research Resources (P41-RR14075, NCRR BIRN002, U24 RR021382)",
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"National Institute for Biomedical Imaging and Bioengineering (R01 EB001550, R01 EB006758, R01 EB009282)",
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"National Institute on Aging (R01 AG02238)",
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"Mental Illness and Neuroscience Discovery (MIND) Institute",
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"National Alliance for Medical Image Computing (NAMIC, U54 EB005149)",
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"The Autism & Dyslexia Project funded by the Ellison Medical Foundation",
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"Centre Hospitalier R\u00e9gional et Universitaire de Tours, Tours, France"
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],
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"ReferencesAndLinks": [
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"https://doi.org/10.1093/cercor/bhg087",
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"https://doi.org/10.1016/j.neuroimage.2010.06.010"
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],
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"Species": "Human",
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"DerivedFrom": "Training set of 12 healthy subjects (24 hemispheres) with high-resolution T1-weighted MPRAGE scans (1.5T Siemens Sonata)",
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"SampleSize": 12,
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"SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-fsaverage_res-1_T1w.nii.gz"
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}

‎atlas-Destrieux/dataset_description.json‎

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

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

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

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