First, you might consider using our 180-area-per-hemisphere functional parcellation (https://balsa.wustl.edu/study/show/RVVG), which is more specialized to human cortex than a distance-based clustering would be. Also keep in mind that vertices being close in 3D doesn't mean they are related, they can be on the opposite side of a large sulcus - we use geodesic distance for this purpose (crawling along the surface triangles). Additional answers inline.
Tim On Tue, Jun 6, 2017 at 4:55 PM, Manasij Venkatesh <mana...@umd.edu> wrote: > Hi, > > The number of vertices on the surface is of the order of ~60k (excluding > subcortical regions). I wish to work in an ROI space (say 100 ROIs) by > clustering the cortical vertices that are near-by. To do so, I need to know > the co-ordinates of the vertices on the surface. I had the following > questions regarding this: > > 1. Does the data in *.dtseries.nii correspond to the time series of the > vertices after surface alignment? If so, which is the file containing the > coordinates of these vertices? > Yes, the coordinates are in ".surf.gii" files. You probably want midthickness coordinates, but there are also pial and white matter surfaces. The MNI space versions are in MNINonLinear/fsaverage_LR32k, but there are also structural space versions (no scaling or stretching from distortion corrected scan data) in the T1w folder. > 2. Do the vertices across patients correspond to the same region in the > brain? > That is the purpose of registration, so fs_LR surfaces have this property, yes. The correspondence is better with MSMAll than with MSMSulc or FreeSurfer. > If this is true, shouldn't there be one surface file for all subjects > after alignment? I'm wondering why there's a surface file for each subject. > No, surface registration does not do anything to anatomical shape. After registration and resampling of a subject's surface, it looks exactly the same as before, it is simply that when we click on a point on one subject's surface, we can now find a matching point on another subject's surface. None of this requires altering the anatomical shape of any subject, so they all still have individual surfaces. One important reason for this is that many functional areas are not strictly matched to nearby sulci/gyri (also, different subjects have rather different folding patterns in a fair portion of cortex). Thus, MSMAll establishes correspondence based on areal features (myelination, visual areas, rfMRI components, cortical thickness), which causes folding patterns to not have as good correspondence across subjects as they would with MSMSulc, which establishes correspondence based only on folding patterns. > Thank you in advance. > > Sincerely, > Manasij > > _______________________________________________ > 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
