Add BEP038-compliant atlas examples of commonly used publicly available atlases #518
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| { | ||
| "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-01_T1w.nii.gz" | ||
| } | ||
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| { | ||
| "Authors": [ | ||
| "N. Tzourio-Mazoyer", | ||
| "B. Landeau", | ||
| "D. Papathanassiou", | ||
| "F. Crivello", | ||
| "O. Etard", | ||
| "N. Delcroix", | ||
| "B. Mazoyer", | ||
| "M. Joliot" | ||
| ], | ||
| "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": "CC BY-SA 4.0", | ||
| "Name": "Automated Anatomical Labeling Atlas", | ||
| "SourceDatasets": [ | ||
| { | ||
| "URL": "https://www.gin.cnrs.fr/en/tools/aal/" | ||
| } | ||
| ] | ||
| } |
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| { | ||
| "Authors": [ | ||
| "Holmes CJ", | ||
| "Hoge R", | ||
| "Collins DL", | ||
| "Woods R", | ||
| "Toga AW", | ||
| "Evans AC" | ||
| ], | ||
| "Curators": [ | ||
| "Esteban O" | ||
| ], | ||
| "Identifier": "MNIColin27", | ||
| "License": "See LICENSE file", | ||
| "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": "Homo sapiens" | ||
| } |
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| index name hemisphere | ||
| 0 Background NA | ||
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| 1 Precentral_L L | ||
| 2 Precentral_R R | ||
| 3 Frontal_Sup_2_L L | ||
| 4 Frontal_Sup_2_R R | ||
| 5 Frontal_Mid_2_L L | ||
| 6 Frontal_Mid_2_R R | ||
| 7 Frontal_Inf_Oper_L L | ||
| 8 Frontal_Inf_Oper_R R | ||
| 9 Frontal_Inf_Tri_L L | ||
| 10 Frontal_Inf_Tri_R R | ||
| 11 Frontal_Inf_Orb_2_L L | ||
| 12 Frontal_Inf_Orb_2_R R | ||
| 13 Rolandic_Oper_L L | ||
| 14 Rolandic_Oper_R R | ||
| 15 Supp_Motor_Area_L L | ||
| 16 Supp_Motor_Area_R R | ||
| 17 Olfactory_L L | ||
| 18 Olfactory_R R | ||
| 19 Frontal_Sup_Medial_L L | ||
| 20 Frontal_Sup_Medial_R R | ||
| 21 Frontal_Med_Orb_L L | ||
| 22 Frontal_Med_Orb_R R | ||
| 23 Rectus_L L | ||
| 24 Rectus_R R | ||
| 25 OFCmed_L L | ||
| 26 OFCmed_R R | ||
| 27 OFCant_L L | ||
| 28 OFCant_R R | ||
| 29 OFCpost_L L | ||
| 30 OFCpost_R R | ||
| 31 OFClat_L L | ||
| 32 OFClat_R R | ||
| 33 Insula_L L | ||
| 34 Insula_R R | ||
| 37 Cingulate_Mid_L L | ||
| 38 Cingulate_Mid_R R | ||
| 39 Cingulate_Post_L L | ||
| 40 Cingulate_Post_R R | ||
| 41 Hippocampus_L L | ||
| 42 Hippocampus_R R | ||
| 43 ParaHippocampal_L L | ||
| 44 ParaHippocampal_R R | ||
| 45 Amygdala_L L | ||
| 46 Amygdala_R R | ||
| 47 Calcarine_L L | ||
| 48 Calcarine_R R | ||
| 49 Cuneus_L L | ||
| 50 Cuneus_R R | ||
| 51 Lingual_L L | ||
| 52 Lingual_R R | ||
| 53 Occipital_Sup_L L | ||
| 54 Occipital_Sup_R R | ||
| 55 Occipital_Mid_L L | ||
| 56 Occipital_Mid_R R | ||
| 57 Occipital_Inf_L L | ||
| 58 Occipital_Inf_R R | ||
| 59 Fusiform_L L | ||
| 60 Fusiform_R R | ||
| 61 Postcentral_L L | ||
| 62 Postcentral_R R | ||
| 63 Parietal_Sup_L L | ||
| 64 Parietal_Sup_R R | ||
| 65 Parietal_Inf_L L | ||
| 66 Parietal_Inf_R R | ||
| 67 SupraMarginal_L L | ||
| 68 SupraMarginal_R R | ||
| 69 Angular_L L | ||
| 70 Angular_R R | ||
| 71 Precuneus_L L | ||
| 72 Precuneus_R R | ||
| 73 Paracentral_Lobule_L L | ||
| 74 Paracentral_Lobule_R L | ||
| 75 Caudate_L L | ||
| 76 Caudate_R R | ||
| 77 Putamen_L L | ||
| 78 Putamen_R R | ||
| 79 Pallidum_L L | ||
| 80 Pallidum_R R | ||
| 83 Heschl_L L | ||
| 84 Heschl_R R | ||
| 85 Temporal_Sup_L L | ||
| 86 Temporal_Sup_R R | ||
| 87 Temporal_Pole_Sup_L L | ||
| 88 Temporal_Pole_Sup_R R | ||
| 89 Temporal_Mid_L L | ||
| 90 Temporal_Mid_R R | ||
| 91 Temporal_Pole_Mid_L L | ||
| 92 Temporal_Pole_Mid_R R | ||
| 93 Temporal_Inf_L L | ||
| 94 Temporal_Inf_R R | ||
| 95 Cerebellum_Crus1_L L | ||
| 96 Cerebellum_Crus1_R R | ||
| 97 Cerebellum_Crus2_L L | ||
| 98 Cerebellum_Crus2_R R | ||
| 99 Cerebellum_3_L L | ||
| 100 Cerebellum_3_R R | ||
| 101 Cerebellum_4_5_L L | ||
| 102 Cerebellum_4_5_R R | ||
| 103 Cerebellum_6_L L | ||
| 104 Cerebellum_6_R R | ||
| 105 Cerebellum_7b_L L | ||
| 106 Cerebellum_7b_R R | ||
| 107 Cerebellum_8_L L | ||
| 108 Cerebellum_8_R R | ||
| 109 Cerebellum_9_L L | ||
| 110 Cerebellum_9_R R | ||
| 111 Cerebellum_10_L L | ||
| 112 Cerebellum_10_R R | ||
| 113 Vermis_1_2 NA | ||
| 114 Vermis_3 NA | ||
| 115 Vermis_4_5 NA | ||
| 116 Vermis_6 NA | ||
| 117 Vermis_7 NA | ||
| 118 Vermis_8 NA | ||
| 119 Vermis_9 NA | ||
| 120 Vermis_10 NA | ||
| 121 Thal_AV_L L | ||
| 122 Thal_AV_R R | ||
| 123 Thal_LP_L L | ||
| 124 Thal_LP_R L | ||
| 125 Thal_VA_L L | ||
| 126 Thal_VA_R R | ||
| 127 Thal_VL_L L | ||
| 128 Thal_VL_R R | ||
| 129 Thal_VPL_L L | ||
| 130 Thal_VPL_R R | ||
| 131 Thal_IL_L L | ||
| 132 Thal_IL_R R | ||
| 133 Thal_Re_L L | ||
| 134 Thal_Re_R R | ||
| 135 Thal_MDm_L L | ||
| 136 Thal_MDm_R R | ||
| 137 Thal_MDl_L L | ||
| 138 Thal_MDl_R R | ||
| 139 Thal_LGN_L L | ||
| 140 Thal_LGN_R L | ||
| 141 Thal_MGN_L L | ||
| 142 Thal_MGN_R R | ||
| 143 Thal_PuI_L L | ||
| 144 Thal_PuI_R R | ||
| 145 Thal_PuM_L L | ||
| 146 Thal_PuM_R R | ||
| 147 Thal_PuA_L L | ||
| 148 Thal_PuA_R R | ||
| 149 Thal_PuL_L L | ||
| 150 Thal_PuL_R R | ||
| 151 ACC_sub_L L | ||
| 152 ACC_sub_R R | ||
| 153 ACC_pre_L L | ||
| 154 ACC_pre_R R | ||
| 155 ACC_sup_L L | ||
| 156 ACC_sup_R R | ||
| 157 N_Acc_L L | ||
| 158 N_Acc_R R | ||
| 159 VTA_L L | ||
| 160 VTA_R R | ||
| 161 SN_pc_L L | ||
| 162 SN_pc_R R | ||
| 163 SN_pr_L L | ||
| 164 SN_pr_R R | ||
| 165 Red_N_L L | ||
| 166 Red_N_R R | ||
| 167 LC_L L | ||
| 168 LC_R R | ||
| 169 Raphe_D NA | ||
| 170 Raphe_M NA | ||
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| { | ||
| "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": "Humans", | ||
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||
| "DerivedFrom": "Training set of 12 healthy subjects (24 hemispheres) with high-resolution T1-weighted MPRAGE scans (1.5T Siemens Sonata)", | ||
| "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-fsaverage_res-01_T1w.nii.gz" | ||
| } | ||
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|---|---|---|
| @@ -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" | ||
| } | ||
| ] | ||
| } |
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|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| { | ||
| "Authors": [], | ||
| "BIDSVersion": "1.1.0", | ||
| "Curators": [ | ||
| "Esteban O" | ||
| ], | ||
| "Identifier": "fsaverage", | ||
| "License": "See LICENSE file", | ||
| "Name": "FreeSurfer's fsaverage template", | ||
| "ReferencesAndLinks": [ | ||
| "https://doi.org/10.1002/(sici)1097-0193(1999)8:4%3C272::aid-hbm10%3E3.0.co;2-4" | ||
| ], | ||
| "Species": "Homo sapiens", | ||
| "TemplateFlowVersion": "1.0.0", | ||
| "res": { | ||
| "01": { | ||
| "origin": [ | ||
| -128.0, | ||
| -128.0, | ||
| -128.0 | ||
| ], | ||
| "shape": [ | ||
| 256, | ||
| 256, | ||
| 256 | ||
| ], | ||
| "zooms": [ | ||
| 1.0, | ||
| 1.0, | ||
| 1.0 | ||
| ] | ||
| }, | ||
| "02": { | ||
| "origin": [ | ||
| -2.0, | ||
| -16.0, | ||
| 9.0 | ||
| ], | ||
| "shape": [ | ||
| 76, | ||
| 76, | ||
| 93 | ||
| ], | ||
| "zooms": [ | ||
| 2.0, | ||
| 2.0, | ||
| 2.0 | ||
| ] | ||
| } | ||
| } | ||
| } |
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