Hi Doug,

I used the caudate surface I created as an example as I was testing the command out. I do not plan to use this command for the caudate. It just happened to show the same issue as the earlier post (https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22\[Freesurfer\]+R+L+flipping%22&o=newest&f=1) and so I thought it would be the clearest way of showing you the issue I was referring to.

I want to flip the lh.thickness.fwhm10.fsaverage.gii files to the right hemisphere for certain subjects and I was worried about having a similar voxel shift if I used mris_reverse. I found posts using xhemireg and surfreg along with mris_reverse, and so I am trying to figure out what is the best way to flip these thickness files to the opposite hemisphere (files already warped to symmetric space)

Thanks,

Ajay

On Mon, Mar 28, 2016 at 5:05 PM, Ajay Kurani <dr.ajay.kurani@gmail.com> wrote:

Hi Doug,
I attached a .png file to show an example. The Yellow outline is the right and left caudate surface. The right surface (yellow) was created by using 3dLRflip (Afni program) to symmetrically flip the volumetric ROI so that I can create the right caudate surface from scratch again. The blue outline is the same right caudate surface created when I used mris_reverse on the left hemisphere surface. As you can see the blue surface outline is not exactly symmetrical, but rather it is shifted to the left by one voxel. This was noted in some earlier posts regarding mris_reverse from 2004 as an issue (https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22\[Freesurfer\]+R+L+flipping%22&o=newest&f=1).

I was curious to see if xhemireg or the surfreg methods alleviate this issue, or if there is another set of preferred commands to symmetrically L-R flip the brain?

Thanks,
Ajay
On Mon, Mar 28, 2016 at 3:03 PM, Ajay Kurani <dr.ajay.kurani@gmail.com> wrote:
Hi Freesurfer Experts,
In testing mris_reverse, there seems to be a voxel shift. In looking up other freesurfer utitlites I came across xhemireg and surfreg.

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-September/040573.html

Does xhemireg or surfreg call out mris_reverse, causing the same pixel shift issue???
Based on what I can find is it best to run the following:
surfreg --s sub001 --t fsaverage_sym --lh --xhemi
Would this flip my lh.thickness.fwhm10.fsaverage_sym.mgh file to the other hemisphere?
Thanks,
Ajay  
On Mon, Mar 28, 2016 at 1:30 PM, Ajay Kurani <dr.ajay.kurani@gmail.com> wrote:
Hello Freesurfer Experts,

I processed all of my brains through freesurfer 6.0 dev for Linux and warped the surfaces to standardized space. For a handful of subjects I want to perform a left right flip of the cortical thickness files (standardized space) for a group analysis. What is the best way to perform this in freesurfer? I have found a previous post referencing mris_reverse but there was a mention of it being off by a voxel when flipped. I wanted to see if this is still a concern with the latest version?

Is there a better way to achieve this goal without rerunning all of freesurfer such as a newer took, or is this the preferred method?

Thanks,
Ajay