Dear FreeSurfers,

I am having some problems creating a label in tksurfer and subsequently converting it into a volume file. I have created a custom label in a test subject using tksurfer which loads correctly onto the surface when viewed with tksurfer. However, when I load the label into tkmedit in the same subject – it seems to be labelling regions that are not on the surface of the brain, but lie somewhat haphazardly in the cortex near the surface. Do you know why this is happening?

I further need to convert the label into a volume file and have used mri_label2vol to do this.

Mri_label2vol -- label subject/label/pfc.label –temp subject/mri/brainmask.mgz  --o subject/label/pfc.mgz

However, perhaps since I can see that the label does not sit correctly on the surface in tkmedit, the volume file is also not on the cortical surface, but runs below it.  Can anyone point me in the right direction as to where I might be going wrong?

Thanks,

Prapti