diff --git a/atlas-sv2a/.bidsignore b/atlas-sv2a/.bidsignore new file mode 100644 index 000000000..2619c0360 --- /dev/null +++ b/atlas-sv2a/.bidsignore @@ -0,0 +1 @@ +atlas-NRUSV2A2024_desc-regionalvalues.tsv diff --git a/atlas-sv2a/atlas-NRUSV2A2024_desc-regionalvalues.tsv b/atlas-sv2a/atlas-NRUSV2A2024_desc-regionalvalues.tsv new file mode 100644 index 000000000..a7ce188dd --- /dev/null +++ b/atlas-sv2a/atlas-NRUSV2A2024_desc-regionalvalues.tsv @@ -0,0 +1,51 @@ +region Vt.mean Vt.sd Bmax.mean Bmax.sd +accumbens.area 19.4258151991962 2.85512637360944 598.420816448135 107.661339416428 +amygdala 16.07065808196 2.23911677180981 471.90427674851 84.4327988389796 +bankssts 20.2977431619254 2.36833163611333 631.299547564821 89.3052435377557 +caudalanteriorcingulate 17.5174813320037 2.36160792528297 526.461206500666 89.0517052984202 +caudalmiddlefrontal 18.5195856504875 2.22425542818111 564.248638314607 83.8724060747984 +caudate 17.8583646255139 2.15447585325547 539.315261684779 81.2411521415773 +cerebellum.cortex 12.6035539975378 1.46699794563979 341.166431630584 55.3176788280168 +cuneus 18.7269113569421 2.25399366086763 572.066493054303 84.9937777914769 +entorhinal 16.5745368879213 2.70192455536405 490.90458008176 101.884392691481 +frontal.cortex 18.6506416139698 2.20692357614855 569.190507332187 83.2188551771427 +frontalpole 18.6663216462181 2.66257570155525 569.781771273968 100.400622885453 +fusiform 18.8682292198663 2.4139304950573 577.395318617515 91.0246890499212 +hippocampus 12.8285160181725 1.69267922920384 349.649317951563 63.8276871745154 +inferiorparietal 19.4198693046626 2.22360175095547 598.196608169502 83.8477571603725 +inferiortemporal 19.3102109461929 2.5925242040285 594.061601796338 97.7591152724915 +insula 18.5698533481906 2.15508350621887 566.144136781544 81.2640655693486 +insular.cortex 18.5722174907285 2.15569706293987 566.233284062224 81.2872016164959 +isthmuscingulate 16.3983179559081 2.05755817201385 484.259702143453 77.5865722700683 +lateraloccipital 17.3549428128519 2.15338441503707 520.33219069233 81.19999609974 +lateralorbitofrontal 18.5254053254637 2.31771713752386 564.468087095821 87.3966678745551 +lingual 18.3984204603919 2.18116152437576 559.679731390936 82.2474176164063 +medialorbitofrontal 18.3865505486824 2.2872000762133 559.232139786861 86.2459280242575 +middletemporal 20.03878231668 2.37767009948325 621.534630777519 89.6573790802624 +occipital.cortex 18.0237257378626 2.16704175323234 545.550712068832 81.7149881283089 +pallidum 11.621611244195 1.37743802488311 304.139253768226 51.9405459922105 +paracentral 17.7308213914338 2.22560900627587 534.505850955539 83.9234469085889 +parahippocampal 17.9006355144517 2.60497842192423 540.909215831056 98.2287399421493 +parietal.cortex 18.860357280734 2.25499914742783 577.098482891214 85.0316927611386 +parsopercularis 20.1369514083647 2.46065457441759 625.236398936633 92.7865644658137 +parsorbitalis 18.8810345347665 2.33527092382081 577.878182481809 88.058587487651 +parstriangularis 19.2997608266113 2.2660502246812 593.667547830248 85.4484076883973 +pericalcarine 18.7732393576307 2.31754955753291 573.813433103166 87.3903487545148 +pons 6.06984427509243 0.785513776712791 94.7927696524158 29.6202179044156 +postcentral 17.4480015684025 2.12606906383857 523.841257877451 80.1699865968879 +posteriorcingulate 18.858166425309 2.35607187720867 577.015869935198 88.8429515436783 +precentral 18.0737878631321 2.11586473908702 547.43845879359 79.7852010824019 +precuneus 19.882694028082 2.33415935807941 615.648840791827 88.0166724755257 +putamen 19.5751349090271 2.33450980748347 604.051376310658 88.0298872503908 +rostralanteriorcingulate 18.5315950594534 2.27895836121268 564.701490092665 85.9351487591935 +rostralmiddlefrontal 18.9430313302344 2.28898227404528 580.215962729048 86.3131312862459 +superiorfrontal 18.6490554099811 2.23449870341626 569.13069462211 84.258660337314 +superiorparietal 17.9336437693127 2.23814541240046 542.153893812031 84.3961707387204 +superiortemporal 19.6269995343782 2.35231027493311 606.007091856293 88.7011087366202 +supramarginal 19.8253633013893 2.44453963135385 613.487009048578 92.1789008713409 +temporal.cortex 19.3476086965355 2.41314993714181 595.471799232872 90.9952557080383 +temporalpole 17.5839394625421 2.77136427535193 528.967215136573 104.502831346841 +thalamus 12.8885869535919 1.44969120869231 351.914477710173 54.6650749720485 +transversetemporal 19.4787409786029 2.26188619400783 600.416546077918 85.2913900783152 +ventraldc 8.06485539265763 0.987635675280807 170.020812464476 37.241847029614 +white.matter 3.87145621278766 0.504062839249118 11.8957723312067 19.0072428755585 diff --git a/atlas-sv2a/atlas-NRUSV2A2024_description.json b/atlas-sv2a/atlas-NRUSV2A2024_description.json new file mode 100644 index 000000000..290d8b198 --- /dev/null +++ b/atlas-sv2a/atlas-NRUSV2A2024_description.json @@ -0,0 +1,24 @@ +{ + "Name": "NRU SV2A Atlas", + "License": "CC-BY-NC-SA-4.0", + "Description": "In vivo high-resolution human synaptic density atlas (SV2A). Converted from the NRU SV2A atlas distribution into a BIDS-style atlas derivatives layout.", + "Authors": [ + "Annette Johansen", + "Vincent Beliveau", + "Emil Colliander", + "Nakul Ravi Raval", + "Vibeke H\u00f8yrup Dam", + "Nic Gillings", + "Susana Aznar", + "Claus Svarer", + "Pontus Plav\u00e9n-Sigray", + "Gitte Moos Knudsen" + ], + "ReferencesAndLinks": [ + "https://xtra.nru.dk/SV2A-atlas/", + "https://doi.org/10.1523/JNEUROSCI.1750-23.2024" + ], + "Species": "Homo sapiens", + "DerivedFrom": "PET", + "LevelType": "group" +} \ No newline at end of file diff --git a/atlas-sv2a/dataset_description.json b/atlas-sv2a/dataset_description.json new file mode 100644 index 000000000..4ce257094 --- /dev/null +++ b/atlas-sv2a/dataset_description.json @@ -0,0 +1,13 @@ +{ + "Name": "NRU SV2A atlas converted to BIDS derivatives", + "BIDSVersion": "1.11.1", + "DatasetType": "derivative", + "License": "CC-BY-NC-SA-4.0", + "GeneratedBy": [ + { + "Name": "convertNRUatlasses.py", + "Version": "1.0.0", + "Description": "Downloads NRU SV2A atlas and renames files to BIDS atlas-derivatives style" + } + ] +} \ No newline at end of file diff --git a/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxCOV_pet.json b/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxCOV_pet.json new file mode 100644 index 000000000..dbaef21e0 --- /dev/null +++ b/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxCOV_pet.json @@ -0,0 +1,7 @@ +{ + "Atlas": "NRUSV2A2024", + "Units": "pmol/mL", + "Source": "NRU SV2A atlas", + "SpatialReference": "MNI152 (as distributed by source atlas)", + "SkullStripped": true +} \ No newline at end of file diff --git a/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxCOV_pet.nii.gz b/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxCOV_pet.nii.gz new file mode 100644 index 000000000..e4cff27c7 Binary files /dev/null and b/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxCOV_pet.nii.gz differ diff --git a/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxMean_pet.json b/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxMean_pet.json new file mode 100644 index 000000000..dbaef21e0 --- /dev/null +++ b/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxMean_pet.json @@ -0,0 +1,7 @@ +{ + "Atlas": "NRUSV2A2024", + "Units": "pmol/mL", + "Source": "NRU SV2A atlas", + "SpatialReference": "MNI152 (as distributed by source atlas)", + "SkullStripped": true +} \ No newline at end of file diff --git a/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxMean_pet.nii.gz b/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxMean_pet.nii.gz new file mode 100644 index 000000000..2840138a7 Binary files /dev/null and b/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxMean_pet.nii.gz differ diff --git a/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxSD_pet.json b/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxSD_pet.json new file mode 100644 index 000000000..dbaef21e0 --- /dev/null +++ b/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxSD_pet.json @@ -0,0 +1,7 @@ +{ + "Atlas": "NRUSV2A2024", + "Units": "pmol/mL", + "Source": "NRU SV2A atlas", + "SpatialReference": "MNI152 (as distributed by source atlas)", + "SkullStripped": true +} \ No newline at end of file diff --git a/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxSD_pet.nii.gz b/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxSD_pet.nii.gz new file mode 100644 index 000000000..e74fcb51d Binary files /dev/null and b/atlas-sv2a/tpl-MNI152/pet/tpl-MNI152_atlas-NRUSV2A2024_desc-BmaxSD_pet.nii.gz differ diff --git a/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxCOV_pet.json b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxCOV_pet.json new file mode 100644 index 000000000..0930ae027 --- /dev/null +++ b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxCOV_pet.json @@ -0,0 +1,7 @@ +{ + "Atlas": "NRUSV2A2024", + "Units": "pmol/mL", + "Source": "NRU SV2A atlas", + "SpatialReference": "fsaverage", + "SkullStripped": true +} \ No newline at end of file diff --git a/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxCOV_pet.nii.gz b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxCOV_pet.nii.gz new file mode 100644 index 000000000..6fa600147 Binary files /dev/null and b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxCOV_pet.nii.gz differ diff --git a/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxMean_pet.json b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxMean_pet.json new file mode 100644 index 000000000..0930ae027 --- /dev/null +++ b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxMean_pet.json @@ -0,0 +1,7 @@ +{ + "Atlas": "NRUSV2A2024", + "Units": "pmol/mL", + "Source": "NRU SV2A atlas", + "SpatialReference": "fsaverage", + "SkullStripped": true +} \ No newline at end of file diff --git a/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxMean_pet.nii.gz b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxMean_pet.nii.gz new file mode 100644 index 000000000..da5a708f2 Binary files /dev/null and b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxMean_pet.nii.gz differ diff --git a/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxSD_pet.json b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxSD_pet.json new file mode 100644 index 000000000..0930ae027 --- /dev/null +++ b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxSD_pet.json @@ -0,0 +1,7 @@ +{ + "Atlas": "NRUSV2A2024", + "Units": "pmol/mL", + "Source": "NRU SV2A atlas", + "SpatialReference": "fsaverage", + "SkullStripped": true +} \ No newline at end of file diff --git a/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxSD_pet.nii.gz b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxSD_pet.nii.gz new file mode 100644 index 000000000..f6827e5b5 Binary files /dev/null and b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-L_atlas-NRUSV2A2024_desc-BmaxSD_pet.nii.gz differ diff --git a/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxCOV_pet.json b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxCOV_pet.json new file mode 100644 index 000000000..0930ae027 --- /dev/null +++ b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxCOV_pet.json @@ -0,0 +1,7 @@ +{ + "Atlas": "NRUSV2A2024", + "Units": "pmol/mL", + "Source": "NRU SV2A atlas", + "SpatialReference": "fsaverage", + "SkullStripped": true +} \ No newline at end of file diff --git a/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxCOV_pet.nii.gz b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxCOV_pet.nii.gz new file mode 100644 index 000000000..46a7b7e70 Binary files /dev/null and b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxCOV_pet.nii.gz differ diff --git a/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxMean_pet.json b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxMean_pet.json new file mode 100644 index 000000000..0930ae027 --- /dev/null +++ b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxMean_pet.json @@ -0,0 +1,7 @@ +{ + "Atlas": "NRUSV2A2024", + "Units": "pmol/mL", + "Source": "NRU SV2A atlas", + "SpatialReference": "fsaverage", + "SkullStripped": true +} \ No newline at end of file diff --git a/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxMean_pet.nii.gz b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxMean_pet.nii.gz new file mode 100644 index 000000000..3deb796a7 Binary files /dev/null and b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxMean_pet.nii.gz differ diff --git a/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxSD_pet.json b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxSD_pet.json new file mode 100644 index 000000000..0930ae027 --- /dev/null +++ b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxSD_pet.json @@ -0,0 +1,7 @@ +{ + "Atlas": "NRUSV2A2024", + "Units": "pmol/mL", + "Source": "NRU SV2A atlas", + "SpatialReference": "fsaverage", + "SkullStripped": true +} \ No newline at end of file diff --git a/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxSD_pet.nii.gz b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxSD_pet.nii.gz new file mode 100644 index 000000000..100e1ff1c Binary files /dev/null and b/atlas-sv2a/tpl-fsaverage/pet/tpl-fsaverage_hemi-R_atlas-NRUSV2A2024_desc-BmaxSD_pet.nii.gz differ