Hi Doug and Bruce, I forgot to mention that I had tried that as well but without success. As a sanity check, tried flipping a label from the 'bert' subject and it still comes out wrong. I've uploaded a screen shot of the result:
https://imgur.com/a/J6Phx Thank you for any input you might have! These were the exact steps the following (I also tried playing around with the options to --streg but without luck): cd ${SUBJECTS_DIR}/bert cd surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right cd ../label mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere $Id: mris_apply_reg.c,v 1.9 2016/12/06 19:40:48 greve Exp $ cwd /home/joe/subjects/bert/label cmdline ../../scripts/mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere sysname Linux hostname computer machine x86_64 user joe srcvalfile (null) trgvalfile lh_flip.BA45.label nsurfs 2 jac 0 revmap 0 1 Loading ../surf/lh.sphere.left_right 2 Loading ../surf/rh.sphere Loading label lh.BA45.label 4060 points in input label MRISapplyReg: nsurfs = 2, revmap=0, jac=0, hash=1 MRISapplyReg: building hash tables (res=16). MRISapplyReg: Forward Loop (133299) MRISapplyReg: Dividing by number of hits (133299) MRISapplyReg: nSrcLost = 38462 4505 points in output label mris_apply_reg done On Thu, Oct 12, 2017 at 5:06 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > Try > > mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg > lh.sphere.left_right rh.sphere > > On 10/11/17 5:43 PM, Neuro Lists 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 > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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. > >
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