Re: [Freesurfer] subcortical mask to MNI152 space

Hi Elisa, sorry about that. Yes, use the $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat instead. doug

Elisa Golfinopoulos wrote:

Hi Doug,

Thanks for responding to my inquiry. My version of Freesurfer (v.5) does not contain

mni152.mni305.cor.subfov2.dat

in the average folder. I did notice that the most recent version of freesurfer has the reg.2mm.mni152.dat

in the same folder as the subcortical mask.

Thanks so much for your help! Take good care. Elisa

On Tue, Jun 7, 2011 at 6:15 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Eventhough they are both in "MNI" space, there is still a
registration that has to be applied. Try something like this:


mri_vol2vol --mov
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz \
 --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
 --reg $FREESURFER_HOME/average/mni152.mni305.cor.subfov2.dat \
--o ./subcort.mask152.nii

Elisa Golfinopoulos wrote:

    Hi,

    I would like to normalize the subcort.mask.mgz to MNI152
    space. I have attempted to use the command:

     mri_vol2vol --mov $FREESURFER_HOME/subjects/
    fsaverage/mri.2mm/subcort.mask.mgz
          --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz
          --o ./subcort.mask152.nii
         --reg $FREESURFER_HOME/average/mni152.register.dat

    but when I check the registration with the MNI152 template I
    find that the 152 normalized subcortical mask does not align
    with the template. The problem is somewhat resolved when I
    specify a 180 degree rotation along the x axis (though there
    still appears to be some translation error). However, I feel
    uncomfortable using rotations/translations without
    understanding why the registration is incorrect in the first
    place.

    In fact, this problem is making me question whether a
    transformation is really necessary since, technically, both
    the mask and the target are in MNI space and the registration
    of the original MNI 305 subcortical mask with the MNI152
    template looks more accurate than the 152 normalized mask. Any
    help that you can offer would be greatly appreciated.

    Cheers,
    Elisa


    -- 
    Elisa Golfinopoulos
    Speech Laboratory
    Cognitive and Neural Systems
    Boston University
    Phone: 617.353.6181 <tel:617.353.6181> <tel:617.353.6181
    <tel:617.353.6181>>

    ------------------------------------------------------------------------

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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>

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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>



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-- Elisa Golfinopoulos Speech Laboratory Cognitive and Neural Systems Boston University Phone: 617.353.6181 tel:617.353.6181