Hi Maria,

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...

Best,

Marie

On Oct 29, 2014, at 10:27 AM, Maria Holland <mholla@stanford.edumailto: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 <Screen Shot 2014-10-29 at 10.23.56 AM.png>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.