The freesurfer segmentation includes a right thalamus definition, among other things, and if you are working in a standard grayordinate space, you can use -cifti-separate with "-volume THALAMUS_RIGHT data_rthal.nii.gz -roi roi_rthal.nii.gz".
Subcortical masks will never be able to be meaningfully mapped onto cortex, they lie outside of cortex. Pick a separate surface ROI of interest or just track to the entire surface. Tim On Tue, Jun 28, 2016 at 9:05 AM, Dev vasu < [email protected]> wrote: > Dear madam, > > > I would like to study the distribution of vestibular tracks from thalamus > to vestibular cortex for which by i would like to define a ROI mask ( > seed mask) from all voxels in the right thalamus and using vestibular > cortex region as target mask. > > > I would first like to create a volume mask and convert them into cortical > surface masks to perform tractography.this is my main goal. I have 30 > subjects ( male ) -from HCP , I have finished with Pre-processing of all > the data now i would like to perform analysis. > > If you have any other better way to map vestibular thalamic connectivity , > i would really appreciate your suggestions. > > > Thanks > Vasudev > > > On 28 June 2016 at 15:50, Dierker, Donna <[email protected]> wrote: > >> Hi Vasudev, >> >> You'll probably need to be more specific about your goals, as there are >> many ways to define a ROI. The most common is to threshold some functional >> map (dscalar.nii or func.gii/nifti) at something like p=.05, but there are >> many other ways to do it. >> >> If you need to draw a ROI manually in workbench, you can load something >> like a curvature, myelin, or functional map and display it in multiple tabs >> or windows (e.g., midthickness surface in one view, very inflated in >> another). You can draw borders on the very inflated map, and see how they >> look on the midthickness. Adjust as needed. >> >> Then wb_command -border-to-rois can fill in the vertices encircled by the >> borders to create a cortical ROI. >> >> For drawing volumetric ROIs, there are all sorts of options out there. >> >> Donna >> >> >> On Jun 27, 2016, at 9:45 AM, Dev vasu < >> [email protected]> wrote: >> >> > Dear Sir, >> > >> > I would like to know how to define structural and functional ROI in >> workbench,should we define the ROI manually ? or is there any alternate >> procedure for it, I am aware of process in SPM but not in workbench. >> > >> > >> > >> > Thanks >> > Vasudev >> > _______________________________________________ >> > 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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
