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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