Dear all
I am segmenting data of 2 year olds and as freesurfer fails on segmneting inferior parts of the temporal lobe, I try to edit this manually using tkmedit (protocol from fswiki: WhiteMatterEdits_tktools, PialEdits_tktools, ControlPoints_tktools). I first add control points, with successfull amelioration of brainmask volumes. As this leads to integration of too much tissue in the white matter surface (displayed as tkmedit brainmask.mgz -surfs), i tried to manually edit wm.mgz. When I edit wm.mgz, there is no change in -surfs. When looking at the data in tkmedit (tkmedit subjid wm.mgz -surfs), total WM surface (-surfs), and wm.mgz are not the same.
Where is the file generated that is shown in tkmedit as -surfs and which volume/file do I have to edit to ameliorate output of -surfs?
Best, Kristina