Thank you for your quick response, that was really helpful. I'll use the 180 parcellations as well, but I wish to do some analysis using custom ROIs.
A quick follow up question: Suppose I want to do clustering using these geodesic distances, is there a file containing them as well? Sincerely, Manasij On Tue, Jun 6, 2017 at 6:12 PM, Timothy Coalson <tsc...@mst.edu> wrote: > 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
