Hi,
The one I tested with in the last couple of messages is just the standard
bert subject after having done:
cd ${SUBJECTS_DIR}/bert
cd surf
mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right
rh.sphere.left_right
And then running:
cd ../label
mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg
../surf/lh.sphere.left_right ../surf/rh.sphere.left_right
Have I misunderstood something?
Thanks again!
On Tue, Oct 17, 2017 at 4:55 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> Is this fsaverage or one of your own subjects?
>
>
>
> On 10/17/2017 02:18 PM, Neuro Lists wrote:
> > 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 <mailto: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
> >> <mailto: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
> >> <mailto: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
> >>>
> >>>
> >>> _______________________________________________
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> >>
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
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