On Thu, Aug 11, 2011 at 3:25 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Catherine

when you say "left" do you mean the left side of the image or the left side of the brain? In tkmedit the left side of the image will always represent the right side of the brain (as indicated by the little green "R" and arrow).

As for the goodness of the surface fit to talairach, that just is a function of the blurriness of the talairach coordinate system.

cheers
Bruce

On Thu, 11 Aug 2011, Catherine Wan wrote:

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

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