Hi Antonella
the atlas is not guaranteed to be correct. If it were we would just take the labels from it :) The only way to tell if it is correct is to look at the segmentations on top of the MR and see if they follow the visible boundary
To get the surfaces you should do
tkmedit SUBJECT1 brainmask.mgz lh.white \ -aux T1.mgz -surfs \ -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt
cheers Bruce
On Tue, 26 Jul 2011, Antonella Kis wrote:
Hi,
I would like to check if my subcortical segmentation is correct so I was running:
tkmedit SUBJECT1 brainmask.mgz \ -aux T1.mgz -surfs \ -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt
1). Pial (red line), and white (yellow line) surfaces are shown and I wonder how I can add a green lie for my orig surface? 2). After I load the aparc+aseg.mgz is theer a way to load and overlay the original/correct atlas so I can see if my segmentation is correct?
Thank you very much. Antonella