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. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
