I have to say that I rarely use freeview, I prefer tkmedit and tksurfer that I know better. So I didn't realize that the images were shifted, I guess it's some preference in how to read the surface. I just tried and have the same kind of shift when using freeview, so I don't think you are doing something wrong. Unless someone else know how to correct for the shift, I would advise you to use tkmedit...

On Oct 29, 2014, at 10:27 AM, Maria Holland <mholla@stanford.edu>

wrote:

Hi Marie -

Thanks for your response. After sending my email I found the hemisphere average values, but the values at each vertex and in each ROI will be very helpful!

I tried the command you provided in tkmedit and it looks perfect - thanks! But when I try what I think is the corresponding command in freeview:

freeview -v <SUBJ>/mri/brainmask.mgz <SUBJ>/mri/T1.mgz -f <SUBJ>/surf/lh.pial-outer-smoothed

the images don't align (see attached). Am I doing something wrong?

~ Maria

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