You should use xhemireg. Just changing the sign of the x coordinate will not be meaningful.
On 03/29/2016 12:49 PM, Ajay Kurani wrote: > 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 > > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C[Freesurfer%5C]+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.kur...@gmail.com > <mailto:dr.ajay.kur...@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 > > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C[Freesurfer%5C]+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.kur...@gmail.com <mailto:dr.ajay.kur...@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.kur...@gmail.com <mailto:dr.ajay.kur...@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 > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list 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.
