So, 2/3 of the spatial locations in HCP CIFTI files are not voxels, only the cerebellum and subcortical structures are represented as voxels. I'm not all that familiar with the structure that ft_read_cifti returns, but it should have the information needed to translate between data matrix indices and voxel indices for the parts that are represented as voxels.
If all else fails, you could use wb_command -cifti-separate with -volume-all to get all the voxel-represented parts in a nifti volume file. There is also -cifti-export-dense-mapping, but those indices do not align with ft_read_cifti, as ft_read_cifti adds NaN values to the data matrix where surface vertices are excluded from the CIFTI file. Using option B of the FAQ entry at https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB? will load the matrix from cifti without altering the indices, but provides no information in matlab about which matrix indices are which vertices/voxels. Tim On Tue, Aug 25, 2015 at 10:06 AM, #LONG HONGQUAN# <long0...@e.ntu.edu.sg> wrote: > Hi HCP Team, > > > Thank you for all the great works that have been done. I am new doing > research in this area and would like to ask a simple question: > > > How do I extract time course for a volume voxel with MNI coordinate from > CIFTI-2 *dtseries.nii file? > > > I am currently using the function ft_read_cifti in cifti-matlab library, > but the data I got does not match with the graph I got from the workbench > view. > > > Also, it seems in workbench v8.3 we could still export the time > series graphs, but I did not find this feature in workbench v1.1.1. > > > Could you give me some suggestions on how to extract the time course for a > single volume if I already have the MNI and IJK coordinate? I prefer to use > Matlab. > > > Thank you. I would really appreciate if you could provide me with some > hints. > > > Best Regards, > > Hongquan Long > > School of Computer Engineering > > Nanyang Technological University > > > > > > _______________________________________________ > 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
