Re: [HCP-Users] Coordinate of CIFTI files

[Glasser, Matthew]

The CIFTI standard space is in MNI space (subcortical voxels).  If you use the surface ${StudyFolder}/${SubjectID}/MNINonLinear/fsaverage_LR32k/${SubjectID}.${Hemisphere}.midthickness.32k_fs_LR.surf.gii, then you will have surface coordinates in MNI space as well.   As for the question about diffusion data, you're going to need to be more specific because I don't know what you are trying to do. Peace, Matt. From: Timothy Coalson <tsc...@mst.edu> Date: Wednesday, August 7, 2013 4:11 PM To: Huang Su-Chun <claire0...@gmail.com> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Coordinate of CIFTI files The volume space that should be used to turn the indices into an XYZ location is in the Volume XML element, which in cifti 1.0 is a child of the Matrix element (ignore the "TransformedSpace" attribute, we don't use it or set it to anything different depending on the space).  The meaning of the XYZ coordinates depends entirely on how the cifti file was generated - just like any volume file, it is possible to set any coordinate system you want.  I believe the cifti files we release in the hcp data have voxels in MNI space via FNIRT. For completeness, cifti files do not contain the surface coordinates, you must get those from the relevant surface file (.surf.gii in the hcp data). Tim On Wed, Aug 7, 2013 at 3:47 PM, Huang Su-Chun <claire0...@gmail.com> wrote: Hello HCP teams, Thank you for all the hard works you did. I have some questions about the coordinate of CIFTI files.  I read the online material and it mentioned that there are node index (for surface), voxel index (for volume), and an XYZ coordinate. My questions is that what space the voxel index is in?  (ex: MNI or Talairach). In the other words, how to transfer the diffusion data from MNI space to the CIFTI nodes and volume space? Also, what's the XYZ coordinate means? Is it in Talairach space? Or individual's anatomy space? Thank you very much for answering these detailed questions, Su -- Su-Chun Huang Research Scientist Integrated Brain Imaging Center Department of Radiology University of Washington Seattle, WA 98195 phone: 206-687-0113 _______________________________________________ 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   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