As you said, the voxels in cifti files are stored by their integer indices as if they were in a volume file, so to get their location in space, you need a transformation matrix, similar to the nifti sform. This is exactly what the TransformationMatrixVoxelIndicesIJKtoXYZ element is. The simple way to explain how to use it is to take the integer voxel indices as a column vector, append a constant of 1 (important, don't use 0, if you get this wrong your coordinates will be shifted but look plausible), and then right multiply the matrix by it. The first 3 elements of the resulting vector are your coordinates.
Note, of course, that 2/3 of the 91k grayordinates space is on surfaces, not represented as voxels, and the coordinates of these points is stored in separate gifti surface files. Tim On Mon, Nov 30, 2015 at 1:02 PM, Rose Tharail John <mailboxofr...@gmail.com> wrote: > Hi all, > > I have extracted the voxel to voxel connectivity correlation matrix from > the 33 gb file HCP_S500_R468_MIGPd4500ROW.dconn.nii, which is a dense > connectivity file. Using the wb_command - *nifti-information -print-xml* I > also pulled out the xml header information within this file. And, I have > with me the Row and Column headers for voxel indices in the file obtained > through the wb_command - *wb_command -cifti-export-dense-mapping*. After > going over the CIFTI-2 documentation I have a query about this field in the > header - *TransformationMatrixVoxelIndicesIJKtoXYZ*. What is the use of > this matrix, and how do I use it? The documentation is not clear about how > to convert from IJK to XYZ. It just mentions the structure of the matrix > and I am unable to think of any matrix operations to apply on IJK indices. > Also, are the voxel indices mentioned in the .nii file, not the actual > voxel coordinates? Should we apply this transformation matrix to obtain > that? > > Any advice will be highly appreciated. > > Thank you. > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
