hmmm, we don't have a caudate surface. How did you make it? mris_reverse just changes the sign on the x coordinate. This might not show up "properly" in freeview; it does not surprise me that it could appear to be 1 voxel off. This was not the intended use of this program. xhemireg will not help. what are you trying to do?
On 03/28/2016 06:05 PM, Ajay Kurani 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.
