Hi again,
I just wanted to revisit this thread to see if I had misunderstood
something or had done something incorrectly?
The commands I used for bert were as follows:
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.left_right
I tried a few different combinations of mris_left_right_register but
without luck.
Thanks!
On Tue, Oct 17, 2017 at 11:55 PM, Neuro Lists <neuro.mailing.li...@gmail.com>
wrote:
>
> 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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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>> <
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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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