Hi Sarah

do you want to look at the surfaces? This can actually be done in freeview if you don't mind messing around with the command line a bit (you can specify offsets and rotations for the surfaces so that you can see the medial wall if you want). Perhaps Ruopeng can comment?

cheers Bruce On Mon, 9 Jun 2014, Jensen, Sarah wrote:

Dear Freesurfers,

I have a question about whether it is possible to check how well each participant in my study lines up with the Freesurfer template in order to check how midline structures were split. I am concerned about how well my ACC ROIs line up with the midline of the brain, and would like to check for cross-hemisphere contamination along the medial wall. I am particularly interested in detecting any potential residual rotation along the Y axis.

I have projected cortical ROIs onto the cortical surface of the average brain using the mri_vol2surf function and then used annotation files for the left and right hemisphere to project my ROIs from the average template into participant's native space using the mri_surf2surf function.

My question is whether it is possible to get an image of how well the fully segmented Freesurfer image lines up with the template? Preferably in an axial view with both hemispheres visible.

Thanks in advance!

Sarah​

Sarah K. G. Jensen Ph.D. Student Department of Psychology Institute of Psychiatry King's College London E-mail: sarah.jensen@kcl.ac.uk Phone: +44 (0)75 2789 3171