################################## CommonCoordinateFrameworks library ################################## Related schema specification: `CommonCoordinateFramework `_ ------------ ------------ AMB-CCF ------- .. admonition:: metadata sheet :@context: @vocab: :@id: https://openminds.om-i.org/instances/commonCoordinateFramework/AMB-CCF :@type: https://openminds.om-i.org/types/CommonCoordinateFramework :abbreviation: AMB CCF :description: The 'Allen Mouse Brain Common Coordinate Framework' is a 3D reconstruction of an averaged adult mouse brain. :fullName: Allen Mouse Brain Common Coordinate Framework :homepage: https://portal.brain-map.org/ :shortName: Allen Mouse Brain CCF :usedTaxon: `musMusculus `_ `BACK TO TOP `_ ------------ BigBrain -------- .. admonition:: metadata sheet :@context: @vocab: :@id: https://openminds.om-i.org/instances/commonCoordinateFramework/BigBrain :@type: https://openminds.om-i.org/types/CommonCoordinateFramework :abbreviation: BigBrain :description: The 'BigBrain Whole-Brain Model' is a 3D reconstruction of a human brain in extremely high resolution. :fullName: BigBrain Whole-Brain Model :homepage: https://bigbrainproject.org/ :shortName: BigBrain Model :usedTaxon: `homoSapiens `_ `BACK TO TOP `_ ------------ MEBRAINStemplate ---------------- .. admonition:: metadata sheet :@context: @vocab: :@id: https://openminds.om-i.org/instances/commonCoordinateFramework/MEBRAINStemplate :@type: https://openminds.om-i.org/types/CommonCoordinateFramework :abbreviation: MEBRAINStemplate :description: The 'MEBRAINS population-based monkey brain template' is a multi-subject based, multi-modal, volume and surface brain template for macaque monkeys. :fullName: MEBRAINS population-based monkey brain template :shortName: MEBRAINS brain template :usedTaxon: `macacaMulatta `_ `BACK TO TOP `_ ------------ MNI-Colin27 ----------- .. admonition:: metadata sheet :@context: @vocab: :@id: https://openminds.om-i.org/instances/commonCoordinateFramework/MNI-Colin27 :@type: https://openminds.om-i.org/types/CommonCoordinateFramework :abbreviation: MNI-Colin27 :description: The 'MNI Colin 27 Average Brain Stereotaxic Registration Model' is a stereotaxic average of 27 T1-weighted MRI scans of the same individual. It was created at the Montreal Neurological Institute (MNI) in a two step process: (1) each of the 27 T1-weighted scans were registered to stereotaxic space using MRITOTAL (an automated volumetric registration procedure) and resampled onto a 1mm grid. All 27 scans were averaged together to create an initial average. (2) The initial average volume was used as a target for a second phase of registration where each original T1-weighted MRI was re-registered in stereotaxic space. This two-step procedure has the advantage of removing the small variance in intra-subject mapping in stereotaxic space associated with the use of a multi-subject average resulting in an average brain stereotaxic registration model with high signal-to-noise ratio and structure definition. :fullName: MNI Colin27 Average Brain Stereotaxic Registration Model :homepage: https://www.mcgill.ca/bic/software/tools-data-analysis/anatomical-mri/atlases :howToCite: Holmes CJ, Hoge R, Collins L, Woods R, Toga AW, and Evans AC; 'Enhancement of MR images using registration for signal averaging.'; J Comput Assist Tomogr; 1998 Mar-Apr; 22(2):324–333. [doi: 10.1097/00004728-199803000-00032](http://dx.doi.org/10.1097/00004728-199803000-00032) Aubert-Broche B, Evans AC, and Collins DL; 'A new improved version of the realistic digital brain phantom'; NeuroImage; 2006 Aug;32(1):138–145. [doi: 10.1016/j.neuroimage.2006.03.052](https://doi.org/10.1016/j.neuroimage.2006.03.052) :shortName: MNI Colin27 Average Brain :usedTaxon: `homoSapiens `_ `BACK TO TOP `_ ------------ MNI-ICBM152 ----------- .. admonition:: metadata sheet :@context: @vocab: :@id: https://openminds.om-i.org/instances/commonCoordinateFramework/MNI-ICBM152 :@type: https://openminds.om-i.org/types/CommonCoordinateFramework :abbreviation: ICBM152 :description: The 'MNI ICBM152 Average Brain Stereotaxic Registration Model' is an average of T1-weighted magnetic resonance imaging (MRI) scans from 152 normative young adults. :fullName: MNI ICBM152 Average Brain Stereotaxic Registration Model :homepage: https://www.mcgill.ca/bic/software/tools-data-analysis/anatomical-mri/atlases :shortName: MNI ICBM152 :usedTaxon: `homoSapiens `_ `BACK TO TOP `_ ------------ MarmosetNMT ----------- .. admonition:: metadata sheet :@context: @vocab: :@id: https://openminds.om-i.org/instances/commonCoordinateFramework/MarmosetNMT :@type: https://openminds.om-i.org/types/CommonCoordinateFramework :abbreviation: MarmosetNMT :description: Stereotactic coordinate space of the coronal plane generated using computational average of histology sections. :fullName: The Marmoset Nencki-Monash Template in Stereotaxic Coordinates :homepage: https://www.marmosetbrain.org/nencki_monash_template :howToCite: Please refer to the template by its RRID:SCR_018367, and cite the publication of the version of the template you have used. :shortName: Marmoset Nencki-Monash Template :usedTaxon: `callithrixJacchus `_ `BACK TO TOP `_ ------------ P-MarmosetBSC-corT ------------------ .. admonition:: metadata sheet :@context: @vocab: :@id: https://openminds.om-i.org/instances/commonCoordinateFramework/P-MarmosetBSC-corT :@type: https://openminds.om-i.org/types/CommonCoordinateFramework :abbreviation: P-MarmosetBSC-corT :description: Stereotactic coordinate space of the coronal plane. :fullName: Paxinos et al. Coronal Template of the Marmoset Brain in Stereotaxic Coordinates :homepage: http://www.neura.edu.au/research/themes/paxinos-group :shortName: Paxinos et al. Stereotaxic Coronal Template (Marmoset Brain) :usedTaxon: `callithrixJacchus `_ `BACK TO TOP `_ ------------ PW-RBSC-corT ------------ .. admonition:: metadata sheet :@context: @vocab: :@id: https://openminds.om-i.org/instances/commonCoordinateFramework/PW-RBSC-corT :@type: https://openminds.om-i.org/types/CommonCoordinateFramework :abbreviation: PW-RBSC-corT :description: Stereotactic coordinate space of the coronal plane. :fullName: Paxinos and Watson's Coronal Template of the Rat Brain in Stereotaxic Coordinates :shortName: Paxinos and Watson's Stereotaxic Coronal Template (Rat Brain) :usedTaxon: `rattusNorvegicus `_ `BACK TO TOP `_ ------------ SwansonSRB ---------- .. admonition:: metadata sheet :@context: @vocab: :@id: https://openminds.om-i.org/instances/commonCoordinateFramework/SwansonSRB :@type: https://openminds.om-i.org/types/CommonCoordinateFramework :abbreviation: SwansonSRB :description: Stereotactic coordinate system derived from the atlas by Paxinos and Watson (1986; ISBN: 0-12-547621-3). :fullName: Swanson's Stereotactic Brain of the Sprague Dawley Rat :shortName: Swanson's Stereotactic Rat Brain :usedTaxon: `rattusNorvegicus `_ `BACK TO TOP `_ ------------ WHSSD ----- .. admonition:: metadata sheet :@context: @vocab: :@id: https://openminds.om-i.org/instances/commonCoordinateFramework/WHSSD :@type: https://openminds.om-i.org/types/CommonCoordinateFramework :abbreviation: WHSSD :description: The 'Waxholm Space of the Sprague Dawley Rat Brain (coordinate space)' employs a continuous three- dimensional Cartesian coordinate system, with its origin set at the decussation of the anterior commissure. :fullName: Waxholm Space of the Sprague Dawley Rat Brain (coordinate space) :homepage: https://www.nitrc.org/projects/whs-sd-atlas :shortName: WHS of the SD Rat Brain :usedTaxon: `rattusNorvegicus `_ `BACK TO TOP `_ ------------ fsLR ---- .. admonition:: metadata sheet :@context: @vocab: :@id: https://openminds.om-i.org/instances/commonCoordinateFramework/fsLR :@type: https://openminds.om-i.org/types/CommonCoordinateFramework :abbreviation: fsLR :description: The 'Unbiased FsAverage Left–Right Hybrid Surface Space' (fsLR) brings the left and right fsaverage surfaces into geographic correspondence using Landmark-SBR ([Van Essen et al. 2011](https://doi.org/10.1093/cercor/bhr291)). :fullName: Unbiased FsAverage Left–Right Hybrid Surface Space :shortName: fsLR Surface Space :usedTaxon: `homoSapiens `_ `BACK TO TOP `_ ------------ fsaverage --------- .. admonition:: metadata sheet :@context: @vocab: :@id: https://openminds.om-i.org/instances/commonCoordinateFramework/fsaverage :@type: https://openminds.om-i.org/types/CommonCoordinateFramework :abbreviation: fsaverage :fullName: FsAverage Surface Space :shortName: FsAverage Surface Space :usedTaxon: `homoSapiens `_ `BACK TO TOP `_ ------------