Re: [Freesurfer] converting labels to MNI space

Thank you Doug and Bruce now everything works and the region is perfectly aligned!

Best Francesca

2015-12-03 18:03 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu:

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
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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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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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