Hi Bruce, Thanks for your reply. The command I used to visualize is: tksurfer SUBJID rh inflated -overlay allruns01.gfeat/cope3.feat/stat/zstat1.nii.gz \ -overlay-reg run01.feat/reg/freesurfer/anat2std.register.dat \ -fthresh 2.3 -fmid 3.3 -fslope 1 -annot aparc.annot what is the option to make the overlay displayed, say, on the pial surface, or on the face that is at the middle of the pial and the white surface? (I don't see a sampling option in tksurfer help.) George
On Feb 5, 2008 3:17 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi George,
there are two different questions here: (1) what anatomical boundary does each surface represent, and (2) how do you sample functional data onto the surface. For (1) the pial surface is indeed the boundary between gray matter and CSF, but for (2) once you choose a sampling strategy (anywhere from gray/white out to pial) the fMRI data can be displayed on any of the surfaces simply as a visualization. Is that clear?
Bruce
On Tue, 5 Feb 2008, George He wrote:
Hi freesurfer experts, It seems to me the pial surface should be the surface of gray matter,
but
when I overlay functional activations on it, it seems to be surface of
white
matter. The reason I think so is that when I load the same activation in both tksurfer and tkmedit, if I click on an activated area (or any point) on the pial surface in tksurfer, save it, and load it in tkmedit, the point will land on the yellow/green lines while the tksurfer and tkmedit show the same
talairach
coordinate for the point. If I click on a point that is on the red line in tkmedit, save it, and
load
it in tksurfer, they (tkmedit and tksurfer) show different talairach coordinates for the points. Question: what is the truth and what should I expect? Thanks, George