Matt, The focus of the project is the resting state data, at this point all of the requests are concerned about these data sets, rfMRI, no other data sets are involved.
As you indicated in your previous e-mail, in rfMRI data 'cross-subject correspondence is maintained through having the same vertex number mean the same anatomical location in each subject.' My basic question remains the same: If I pick up one grayordinate, I would like to know analytically or in a Cartesian manner which anatomic vertex or voxel this grayordinate belongs to. I would like have the location information of the grayordinate on the 91x109x91 data set, which has cross-subject correspondence. Stated in an another manner, when I load the whole grayordinate data with home build code, it is a bunch of time series but I don't exactly know which series belong to which anatomical location. This becomes extremely important when one wants to automatically chose regions of interest around a voxel. To be able to pick neighbors using grayordinates, I need to know where the neighbors are located in grayordinates. For example, from the grayordinate description in your paper, it is quite possible to jump from left cortex to the right cortex by incrementing by one around the 30Kth grayordinate. Surely, those voxels are not neighbors. I went through the discussion list. There are suggestions that point to moving back and forth between software (e.g., freesurfer, workbench etc.) when selections are hand made. In my case, this will not be feasible as I am trying to home build an automated pipeline. So a translation table defining rigorously seems to be the appropriate solution. Grayordinates are extremely useful. In addition to space saving, thanks to them the need to run cortex segmentation algorithms have been eliminated. This also eliminated potential ambiguities that would be created by various segmentation algorithms. This is in the same spirit as the atlas registered fMRI data for the connectome project. For the grayordinates to reach their full potential, it would be really helpful to have their Cartesian description available. As the grayordinate data are constructed from the 91x109x91 full set by way of a mask(?) and appropriate ordering afterwords, I am hoping that this will not be a big bother. With my apologies for the iteration, I was wondering if there is a translation available in a general readable format such as the ones I indicated earlier: translation table, for example 42,50,50 ---> 1st entry in grayordinates 43,50,50 ---> 2nd entry in grayordinates or a 91x109x91 mask containing grayordinate numbers at the appropiate voxels and zeros elsewhere or any other appropriate common format. thanks in advance for your help, Alpay On 27-Mar-15 12:44, Glasser, Matthew wrote: > 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" <al...@vt.edu> 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" <al...@vt.edu> 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 >>>> HCP-Users@humanconnectome.org >>>> 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 >> HCP-Users@humanconnectome.org >> 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
