oops, gave you the wrong option, it should be

--regheader $SUBJECTS_DIR/mni152-recon/mri/orig.mgz



On 12/03/2015 10:22 AM, Francesca Strappini wrote:
> Thanks!
>
> I run this command:
>
> mri_label2vol --label lh.V1dorsalLG_MNI.label --temp
> /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --regheader
> /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
> lh.V1dorsalLG_MNI.nii.gz
>
> but unfortunately, it gave me the same big downward shift (I checked
> it with fslview).
>
> But if  I try to open the ROI with freeview it gives me this error:
> freeview.bin: empty label
> LabelRead failed
> freeview.bin: empty label
>
> 2015-12-03 16:57 GMT+02:00 Douglas Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>:
>
>     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 <mailto: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 <tel:%2B972%2058%20444%202584>
>>         > E-mail: francesca.strappini@weizmann.ac.il
>>         <mailto:francesca.strappini@weizmann.ac.il>
>>         > <mailto:francesca.strappini@weizmann.ac.il
>>         <mailto:francesca.strappini@weizmann.ac.il>>
>>         >
>>         >
>>         > _______________________________________________
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>>
>>         --
>>         Douglas N. Greve, Ph.D.
>>         MGH-NMR Center
>>         greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>>         Phone Number: 617-724-2358 <tel:617-724-2358>
>>         Fax: 617-726-7422 <tel:617-726-7422>
>>
>>         Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>         <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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>>         www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>         <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>>         Outgoing:
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>>
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>>         <mailto:Freesurfer@nmr.mgh.harvard.edu>
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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
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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 <tel:%2B972%2058%20444%202584>
>>     E-mail: francesca.strappini@weizmann.ac.il
>>     <mailto:francesca.strappini@weizmann.ac.il>
>>
>>
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>
>
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>     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.
>
>
>
>
> --
> 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
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/

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