You are correct, surf2surf is not changing the values from out side the masked region. However the problem is that in smoothing the values inside the masked region surf2surf appears to be incorporating values from outside the masked region (even if its not smoothing these "outside" values).
What I would like to do is to restrict surf2surf to smoothing only within the mask and not use any values that lie outside of it.
I apologize if I'm being unclear, I'm at a bit of a loss for out to accurately describe this.
Thanks, Greg
On Thu, 14 May 2009, Douglas N Greve wrote:
mri_surf2surf will not change the values outside of the mask (those will be left unsmoothed). Is there an actual difference in the mask?
doug
Gregory Dierksen wrote:
Hi,
I want to smooth a cortical thickness map using values only in a specific area. Basically I want to mask out all other segmentations, for example smooth with fwhm of 20 only in the postcentral region.
I've used quite a few combinations of the -label-src and -label-trg flags and noticed a slight problem:
Using the command line (which seems to give the "best" results):
mri_surf2surf --hemi rh --s fsaverage --sval ./rh.Input.mgh --fwhm 20 --label-trg ./postcentral.label --tval rh.Output.mgz
When the rh.Input.mgh has been masked before running surf2surf using postcentral.label (so only the postcentral region is non-zero), I get DIFFERENT values than if rh.Input.mgh is NOT previously masked by postcentral.label (ie ALL verticies have non-zero values inside and outside postcentral region).
How can I get mri_surf2surf (or perhaps some other command) to smooth only within a specified region without taking values from outside this region?
Thanks for the help,
Greg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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