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 list
Freesurfer@nmr.mgh.harvard.edu
https://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.
