Hi all,
My team has recently completed a few hundred FreeSurfer runs on young (2-4 year old) children. For the past month or so, we have been using various editing techniques in order to fix different problems with the white matter volumes (these were to be expected considering the ages of our subjects). Since our goal is to get accurate measurements of cortical thickness, this is a crucial step.
A few of the images simply stop including the white matter at a certain point, always always toward the posterior/occipital region of the brain. We devised an approach to solving this problem that involves converting formats and orientations, loading the brainmask and white matter volume into a manual brain segmentation editing tool, and using a 'snake tool' that fills in the white matter that was not captured by FreeSurfer. We have ensured that the label we used to fill this in is the same as the label used for manual editing within tkmedit. HOWEVER, after rerunning FreeSurfer with this edited volume (using -autorecon2-wm), the surfaces do not seem to have changed at all.
Am I missing something here? I thought that if white matter edits were made that filled in gaps in the original wm.mgz volume, FreeSurfer would adjust the the surfaces accordingly.
I've attached two photos to give you an idea of what I'm experiencing.
Thanks for any advice on this predicament.
Ryan
