{"action":"created","issue":{"url":"https://api.github.com/repos/incf-nidash/nidm/issues/284","labels_url":"https://api.github.com/repos/incf-nidash/nidm/issues/284/labels{/name}","comments_url":"https://api.github.com/repos/incf-nidash/nidm/issues/284/comments","events_url":"https://api.github.com/repos/incf-nidash/nidm/issues/284/events","html_url":"https://github.com/incf-nidash/nidm/pull/284","id":65721372,"number":284,"title":"Definition of \"coordinate system\" terms","user":{"login":"cmaumet","id":5374264,"avatar_url":"https://avatars.githubusercontent.com/u/5374264?v=3","gravatar_id":"","url":"https://api.github.com/users/cmaumet","html_url":"https://github.com/cmaumet","followers_url":"https://api.github.com/users/cmaumet/followers","following_url":"https://api.github.com/users/cmaumet/following{/other_user}","gists_url":"https://api.github.com/users/cmaumet/gists{/gist_id}","starred_url":"https://api.github.com/users/cmaumet/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmaumet/subscriptions","organizations_url":"https://api.github.com/users/cmaumet/orgs","repos_url":"https://api.github.com/users/cmaumet/repos","events_url":"https://api.github.com/users/cmaumet/events{/privacy}","received_events_url":"https://api.github.com/users/cmaumet/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/incf-nidash/nidm/labels/nidm-results","name":"nidm-results","color":"f7c6c7"},{"url":"https://api.github.com/repos/incf-nidash/nidm/labels/Terms","name":"Terms","color":"bfdadc"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-04-01T16:14:21Z","updated_at":"2015-04-20T12:44:12Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/incf-nidash/nidm/pulls/284","html_url":"https://github.com/incf-nidash/nidm/pull/284","diff_url":"https://github.com/incf-nidash/nidm/pull/284.diff","patch_url":"https://github.com/incf-nidash/nidm/pull/284.patch"},"body":"Following #52 and #123, this issue is open to curate the definitions of the terms used to model coordinate systems.\r\n\r\nFirst, let's define the parent class and its associated object property:\r\n - **nidm:WorldCoordinateSystem**: reference space on which real-world positions are expressed (cf. [Nifti-1 FAQ question 14](http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q14) and [Understanding affines on nipy](http://nipy.org/nipy/stable/devel/code_discussions/understanding_affines.html)\r\n). A world coordinate system can be represented by an image obtained by registering an initial set of images, using a given normalization algorithm to match a target template.\r\n - **nidm:inWorldCoordinateSystem**: Property that associates a world coordinate system to the coordinate space.\r\n\r\nTerms *in italics* are individuals, **in bold** are classes:\r\n  - ~~nidm:StandardizedCoordinateSystem~~\r\n  \r\n  - *nidm:TalairachCoordinateSystem*: Reference space defined by the dissected brain used for the Talairach and Tournoux atlas (cf. http://www.talairach.org/about.html).\r\n  \r\n\r\n  - **nidm:MNICoordinateSystem**: MNI 305 coordinate system or any coordinate system derived from MNI 305. \r\n    \r\n    - *nidm:Mni305CoordinateSystem*: Reference space defined as the average of 305 T1-weighted MRI scans, linearly transformed to Talairach space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/MNI305 for more details).\r\n\r\n    - *nidm:IcbmMni152LinearCoordinateSystem*: Reference space which is the average of 152 T1-weighted MRI scans, linearly transformed onto the MNI 305 reference space (definition adapted from: http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin). This is the default in SPM99 to SPM8 (cf. [MRC CBSU Wiki](http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach) and `spm8/spm_templates.man`.\r\n\r\n    -  *nidm:IcbmMni152NonLinear2009aSymmetricCoordinateSystem*: Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to to form a symmetric model in MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details).\r\n    -  *nidm:IcbmMni152NonLinear2009aAsymmetricCoordinateSystem*: Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details).\r\n    -  *nidm:IcbmMni152NonLinear2009bSymmetricCoordinateSystem*: Reference space defined as the average of 152 T1-weighted MRI scans in high-resolution, non-linearly transformed to form a symmetric model in MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details).         \r\n    -  *nidm:IcbmMni152NonLinear2009bAsymmetricCoordinateSystem*: Reference space defined as the average of 152 T1-weighted MRI scans in high-resolution, non-linearly transformed to MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details).\r\n    -  *nidm:IcbmMni152NonLinear2009cSymmetricCoordinateSystem*: Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to form a symmetric model in MNI152 linear space using the N3 algorithm (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details). This is the default for DARTEL toolbox in SPM12b (cf. spm12/spm_templates.man).\r\n    -  *nidm:IcbmMni152NonLinear2009cAsymmetricCoordinateSystem*: Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space using the N3 algorithm (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details).\r\n      \r\n    - *nidm:IcbmMni152NonLinear6thGenerationCoordinateSystem*: Reference space defined as the average of 152 T1-weighted MRI scans, linearly and non-linearly (6 iterations) transformed to form a symmetric model in Talairach space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6)\"\r\n     \r\n    - *nidm:Icbm452AirCoordinateSystem*: Reference space defined as the average of 452 T1-weighted MRIs of normal young adult brains after 12 parameter AIR linear transform to the MNI 305 space (cf. http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml and http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)\r\n    - *nidm:Icbm452Warp5CoordinateSystem*: Reference space defined as the average of 452 T1-weighted MRIs of normal young adult brains after affine and 5 order polynomial non-linear warping to the MNI 305 space (cf. http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml and http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)\r\n     \r\n    - *nidm:Ixi549CoordinateSystem*: Reference space defined by the average of the 549 subjects from the IXI dataset linearly transformed to the ICBM MNI 452 (cf. spm12/spm\\_templates.man and http://biomedic.doc.ic.ac.uk/brain-development/index.php?n=Main.Datasets). This is the default in SPM12 (cf. spm12/spm_templates.man).\r\n\r\n  - *nidm:Colin27CoordinateSystem*: Reference space defined as the stereotaxic average of 27 T1-weighted MRI scans of the same individual transformed into the Talairach stereotaxic space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres and http://neuro.debian.net/pkgs/mni-colin27-nifti.html). This is the default in SPM96 (cf. [MRC CBSU Wiki](http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)).\r\n   \r\n  - **nidm:CustomCoordinateSystem**: Custom (unknown) reference space selected by the user.\r\n    \r\n  - **nidm:SubjectCoordinateSystem**: Reference space corresponding to the subject brain (no spatial normalisation applied).\r\n\r\nNote: these definitions mostly come from the table discussed in #52. \r\n\r\nPlease let me know what you think. Thank you!"},"comment":{"url":"https://api.github.com/repos/incf-nidash/nidm/issues/comments/94442357","html_url":"https://github.com/incf-nidash/nidm/pull/284#issuecomment-94442357","issue_url":"https://api.github.com/repos/incf-nidash/nidm/issues/284","id":94442357,"user":{"login":"cmaumet","id":5374264,"avatar_url":"https://avatars.githubusercontent.com/u/5374264?v=3","gravatar_id":"","url":"https://api.github.com/users/cmaumet","html_url":"https://github.com/cmaumet","followers_url":"https://api.github.com/users/cmaumet/followers","following_url":"https://api.github.com/users/cmaumet/following{/other_user}","gists_url":"https://api.github.com/users/cmaumet/gists{/gist_id}","starred_url":"https://api.github.com/users/cmaumet/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmaumet/subscriptions","organizations_url":"https://api.github.com/users/cmaumet/orgs","repos_url":"https://api.github.com/users/cmaumet/repos","events_url":"https://api.github.com/users/cmaumet/events{/privacy}","received_events_url":"https://api.github.com/users/cmaumet/received_events","type":"User","site_admin":false},"created_at":"2015-04-20T12:44:12Z","updated_at":"2015-04-20T12:44:12Z","body":"Thank you! Now implemented and ready to go."}}