On Tue, Oct 17, 2017 at 4:55 PM, Douglas N Greve <greve@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
> <greve@nmr.mgh.harvard.edu <mailto:greve@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.lists@gmail.com

>> <mailto:neuro.mailing.lists@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
>> <greve@nmr.mgh.harvard.edu

>> <mailto:greve@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
greve@nmr.mgh.harvard.edu
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