I think mri_label2label with the sphere from the left right registration should work Bruce
> On Oct 11, 2017, at 5:43 PM, Neuro Lists <neuro.mailing.li...@gmail.com> > wrote: > > Hi all, > I've searched the lists extensively and have not been able to resolve my > problem. I'd greatly appreciated any help. > > I have run the recon-all pipeline on a number of subjects, made the > appropriate fixes and am happy with the surfaces. For each subject, I have a > number of ROIs that are created programmatically and they are exactly as they > should be. These ROIs are on the "regular" surfaces, not the inflated ones. > In other words, opening the brainmask.mgz in freeview and just loading the > label file results in the ROI being where I expect it to be. > > > I'm now trying to flip the ROI onto the contralateral hemisphere and this is > going terribly wrong. No matter what I try, the ROI ends up being generated > far outside of the brain. > > > I was originally trying to use the xhemi pipeline, but then I realized from > the forums that I could just use mris_left_right_register. > > I've done: > > cd subject/surf > mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right > rh.sphere.left_right > > I've then tried using a number of varieties of mri_apply_reg that have been > listed on the forum: > 1) mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg > lh.sphere lh.sphere.left_right > 2) mris_apply_reg --src-label lh.source.label --streg lh.sphere.left_right > rh.sphere.left_right --trg rh.lh.source.label > > > No matter what I try though, the flipped ROI ends up being way outside of the > brain when I overlay it on the brainmask. Is this because the flipped ROI > should instead be visualized on the inflated hemisphere? If so, how can I get > it to overlay properly onto the brainmask so that I can be sure it's correct? > My ultimate goal is to get anatomical stats from the original and flipped > ROIs. > > > Thanks for your help! > > Joe > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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