Hi Nima,

the surfaces are "frozen" when they are adjacent to non-cortical regions, as determined by the aseg. Are the regions where it is (incorrectly) deforming segmented properly? Control points definitely won't help, and you can't add them for the pial surface really (although adding them to the white matter can fix pial surface problems, particularly if the wm.mgz is made more accurate by them).

cheers, Bruce

On Tue, 29 Jan 2008 nima@nmr.mgh.harvard.edu wrote:

Hi Guys, In few recons, I noitced that in the midline, pial and white matter boundaries are not the way they are supposed to be; i.e., they sometimes diverge toward the ventricles instead of following the midline and these divergences are not symmetrical either. I thought maybe I should add some cp...but that does not make sense because in actuality there is not white matter there as it is underneath the cortical gray matter... Any suggestion?

The new version of the freesurfer fills the 3rd ventricle adjacent to the fornices. Should I leave the fornices in? or I should clean it up like old versions?

ps. is there any way to add control points for pial surface?

cheers nima _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer