Try adding --invertmtx to the mri_label2vol command. I don't think the label2label command does anything, does it? Also, you might have better alignment if you run recon-all on the mni152 brain, then use mri_label2label to map the label from the individual into the 152 space using the surface transform, then convert that to the volume.
On 11/30/2015 10:13 AM, Francesca Strappini wrote:
Dear FreeSurfer experts,
I'm trying to convert some retinotopic labels I created on the surface of each individual subject to MNI305 space for FSL.
I run the following commands, but the output is not registered correctly. It seems to be shifted downward.
mni152reg --s LG
mri_label2label --srclabel lh.V1dorsalLG.label --s LG --regmethod surface --trglabel lh.V1dorsalLG_new.label --hemi lh
mri_label2vol --label lh.V1dorsalLG_new.label --reg /usr/local/freesurfer/subjects/LG/mri/mni152.orig.mgz.reg --temp /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o lh.V1dorsalLG_new_MNI.nii.gz
Thanks for your help, Francesca
-- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini@weizmann.ac.il mailto:francesca.strappini@weizmann.ac.il
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