p.s. note that the image you show of the surface over the tal volume has a caption saying "surface registration", but in fact what you are showing is the talairach (volume) registration applied to the surface, *not* the surface registration. The easiest way to check the surface registration is to look at the accuracy of the ?h.aparc.annot. If it looks good then the surface registration worked.
On Thu, 11 Aug 2011, Catherine Wan wrote:
Dear Freesurfer-list,
I have 2 questions: one regarding lesioned brains and another regarding kids? brains.
- All of our patients have large lesions on the left side. After the recon-all step, I used tkmedit brainmask.mgz and found that for some patients, the lesion location
had been flipped from left to right (see attached). Any suggestions on how to solve this issue, prior to running a group level analysis?
- We have preprocessed some images of typically-developing children (9-11yo). After recon-all, I checked the registration using tkregister2 --mgz ?s--fstal --surf orig and
found that the green line didn?t cover the surfaces well in most cases (see attached) . I?ve read in previous postings that Freesurfer should be fine with kids? brains, so perhaps we don't need to modify them manually? Is there any other way to check for registration? Any other suggestions?
Many thanks in advance for your help!
Regards, Catherine