Okay, but be aware that the volume registration isn't perfect even for subcortical structures. We go to some trouble to deal with the non-overlapping edges without mixing data across individually-identified subcortical structures when we put subcortical data into CIFTI. I don't know how bad the non-overlapping edges get in the thalamus, there may only be a few subcortical structures where this problem is significant.
Tim On Thu, Feb 22, 2018 at 2:50 AM, Claude Bajada <c.baj...@fz-juelich.de> wrote: > Thanks Tim and Ely, > > This is helpful. > > Tim, I think I prefer your second suggestion (using the standard cifti > MNINonLinear group definition). I need a one to one correspondence between > every point in the thalamus across individuals and to a template thalamus. > The reason (and perhaps I need to go into more detail of what I hope to do) > is that I would like to perform tractography seeding from every voxel > (independently) in the thalamus and then be able to project any statistics > that are derived from those tracts back onto the thalamus itself. I would > like the correspondence from beforehand since I would like to do all the > projections directly onto the template thalamus in MNI space. I also do not > really need native voxels but only a centroid coordinate for each template > voxel in native space; since I use mrtrix for my tractography. > > I am also looking for the subjects' atlas warpfields but cannot seem to > find them could you point me in the right direction/directory? > > Cheers, > > Claude > > On il-Ħamis, 22 ta Fra, 2018 01:07 , Timothy Coalson wrote: > > 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 <c.baj...@fz-juelich.de> > 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 >> 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
