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