Dear Bruce Yeah, exactly! Is there another command I should run? Best, Kristina ________________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Dienstag, 13. Mai 2014 14:35 An: Freesurfer support list Betreff: Re: [Freesurfer] white matter surface (tkmedit -surfs) vs wm.mgz
Hi Kristina
are you running:
recon-all -autorecon2-cp -autorecon3 ...
after adding control points and editing the wm?
Bruce On Tue, 13 May 2014, Mayer Kristina wrote:
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
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