Hi Doug, Thanks a lot for looking into it. Unfortunately it's still not working though.
See here: https://imgur.com/a/lxXUH Thanks again! On Mon, Oct 16, 2017 at 12:31 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > Sorry, try this > > mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg > ../surf/lh.sphere.left_right ../surf/rh.sphere.left_right > > On 10/13/17 2:58 PM, Neuro Lists wrote: > > Hi all, > I was just wondering if there was any further insight into what I might be > doing wrong on this. > > Thanks again! > > > > On Thu, Oct 12, 2017 at 10:30 AM, Neuro Lists < > neuro.mailing.li...@gmail.com> wrote: > >> 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. >>> >>> >> > > > _______________________________________________ > 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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