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. >> >> >
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