Dear Freesurfer-list,
I have 2 questions: one regarding lesioned brains and another regarding kids’ brains.
1) 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?
2) 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
