Use --regheader /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz instead of --identity

On 12/3/15 8:46 AM, Francesca Strappini wrote:

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>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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--

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

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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.