That will depend on the surface you choose to use, as the cortical grayordinates are particular surface vertices on a standard surface mesh topology. The 3D volume coordinates of these vertices can change across subjects, but cross-subject correspondence is maintained through having the same vertex number mean the same anatomical location in each subject. Perhaps you can give me some more details on what you are doing and I can be more helpful then.
Peace, Matt. On 3/27/15, 11:25 AM, "Alpay Özcan" <[email protected]> wrote: >Matt, >thank you for your quick reply. > >Just to clarify, my original question was not implying anything >negative about the grayordinates nor any desire to work in MNI space. >In fact, in my view, grayordinates are logically addressing many space >constraints and analysis problems appropriately. > >To rephrase the question, I would like to obtain the definition >of the grayordinates in 91x109x91 volume. The description does not need >to be in the form of a matrix, e.g., a coordinate translation map would >do. For example (I am making up the numbers): > >42,50,50 ---> 1st entry in grayordinates >43,50,50 ---> 2nd entry in grayordinates >etc. > >This is more rigorous than, for instance, saying the grayordinates start >from somewhere in the left cortex. The translation map would help a lot >when CIFTI data are analyzed as you suggested in your reply. > >I hope this is not a big bother. > >thanks again, > >Alpay Özcan, D.Sc. >Research Assistant Professor >Arlington Innovation Center: >Health Research >Virginia Polytechnic Institute >and State University >900 N. Glebe Road >Arlington VA, 22203, USA > >Tel: (571) 858-3204 >http://aic.ncr.vt.edu/~alpay > >On 27-Mar-15 11:54, Glasser, Matthew wrote: >> The whole point of grayordinates is not to work in MNI volume space, but >> to work in a combined cortical surface and subcortical volume space with >> better grayordiante-wise correspondence across subjects. The >>improvements >> gained with grayordinates are simply not possible to achieve in MNI >>volume >> space (for sheet-like cortical regions) because of the differences in >> geometry between a sheetlike structure and a globular nucleus and the >>fact >> that people simply don¹t have topologically corresponding folding >>patterns >> over most of the brain and areas are not always on the same places on >> folds. >> >> If your analysis does not require explicit spatial neighborhood >> information (most kinds of analysis do not require this) you can simply >> analyze the CIFTI data as a matrix (which you can convert to and from >> CIFTI and other formats like NIFTI using wb_command -cifti-convert). >>For >> example, one can run FSL¹s melodic tool (which does not support CIFTI >>but >> also does not care about spatial neighborhood relationships) by >>converting >> the CIFTI data to NIFTI, running melodic, and then converting the >>results >> from NIFTI back to CIFTI. If you do require explicit spatial >>neighborhood >> information, have a look at the commands available in wb_command that >>work >> natively on CIFTI files (e.g. finding clusters, smoothing, gradients, >> etc.), or write your own (you will need to interpret the surface >>topology >> of the 32k standard meshes). >> >> Peace, >> >> Matt. >> >> On 3/27/15, 10:42 AM, "Alpay Özcan" <[email protected]> wrote: >> >>> Hello, >>> There is a need for understanding where exactly grayordinates locations >>> are placed. The descriptions in the Neuroimage 80 papers (Glasser et. >>> al) are nice and helpful but for computational purposes an analytical >>> definition is necessary. My search for such definition of the >>> grayordinates did not yield much. >>> >>> With my apologies in advance if the solution already exists, would it >>>be >>> possible to generate a coordinate volume cube (or 3D matrix) in the MNI >>> space 91x109x91 where the voxel with the 1st grayordinates will have a >>> value of 1, 2nd grayordinates have a value 2, 3rd 3 etc. and the >>> non-grayordinate voxels will have 0 values? >>> >>> An accessible format (raw, NIFTI) would also be extremely helpful. >>> >>> If there is already a solution, pointers will be appreciated. >>> >>> Thanks in advance for your help. >>> >>> Best regards, >>> >>> -- >>> Alpay Özcan, D.Sc. >>> Research Assistant Professor >>> Arlington Innovation Center: >>> Health Research >>> Virginia Polytechnic Institute >>> and State University >>> 900 N. Glebe Road >>> Arlington VA, 22203, USA >>> >>> Tel: (571) 858-3204 >>> http://aic.ncr.vt.edu/~alpay >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> ________________________________ >> The materials in this message are private and may contain Protected >>Healthcare Information or other information of a sensitive nature. If >>you are not the intended recipient, be advised that any unauthorized >>use, disclosure, copying or the taking of any action in reliance on the >>contents of this information is strictly prohibited. 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