It may be better to use the individual subject's "native space" definitions. The files in the T1w folder are in what we refer to as native volume space (it is actually rigidly-aligned MNI space, but rigid alignment preserves shape, so it can be used as if it were distortion-corrected scanner coordinates, after the appropriate resamplings). There are aparc*+aseg.nii.gz files in that folder, which should be the freesurfer segmentation/parcellation for that single subject, which contains a thalamus definition.
If you prefer to use our standard cifti MNINonLinear group thalamus definition, and work that backwards through each subject's atlas warpfield, you can get the entire ROI of left and right thalamus by using -cifti-separate with -volume THALAMUS_LEFT <junk> -roi <roi-output> (and similar with RIGHT) on any small full-brain cifti file (91282 grayordinates for 3T data), for instance the template in the Pipelines at global/templates/91282_Greyordinates/91282_Greyordinates.dscalar.nii . Tim On Wed, Feb 21, 2018 at 3:24 AM, Claude Bajada <[email protected]> wrote: > Dear all, > > I would like to perform tractography seeding from the thalamus. So as to > ensure that I have correspondence between individuals, I would like to > use the thalamus defined in terms of the brainordinates already used in > each participant. > > I cannot find a way to identify the brainordinates that define the > thalamus and extract their voxels / MNI coordinates. Can someone point > me in the right direction? > > Regards, > > Claude > > > > ------------------------------------------------------------ > ------------------------------------ > ------------------------------------------------------------ > ------------------------------------ > Forschungszentrum Juelich GmbH > 52425 Juelich > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > ------------------------------------------------------------ > ------------------------------------ > ------------------------------------------------------------ > ------------------------------------ > > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
