Thank you!
I run the recon-all on the MNI brain and now the first step, label2label, produced a label which is perfectly mapped on the surface of the MNI template. I tried to run the second step, mapping the new label to the volume, but I still got the shift downward.
mri_label2vol --label lh.V1dorsalLG_MNI.label --temp /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o lh.V1dorsalLG_MNI.nii.gz --identity
Best Francesca
2015-12-01 20:26 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.