Hi Doug,

Yes I did and the registration looks good to me (no axial shift in the images) - but I am little confused. In the command for check the registration:

tkregister2 --mov $SUBJECTS_DIR/568/mri/mni152.orig.mgz \
                    --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz \
                    --reg $SUBJECTS_DIR/568/mri/mni152.orig.mgz.reg

I am comparing images of subject in MNI space and the MNI template, right? Why there is also the registration file?

In mri_label2vol I am using /mri/transforms/reg.mni152.2mm.dat for tranform aparc+aseg to MNI. Which transformation to use? Or should I combine somehow the transformations?  The result with the ..transforms/reg.mni152.2mm.dat is still shifted.

Or should I try some other way to get aparc+aseg to MNI?

Thank you for any help,

Matyas
 
PhD student,
CEITEC MU, Brno
Czech republic

Did you verify that the result of mni152reg is accurate? It should have 
printed out a command line to check it


On 9/9/16 5:58 AM, Matyáš Kuhn wrote:

Hi FreeSurfer experts,

We would like to use Destrieux atlas for masking DLPFC in subjects, who
uderwent fMRI and we used SPM to process the data. We want to find peaks
in individuals according to some regions from the atlas (create
individual mask). The problem I am facing is to get
aparc.a2009s+aseg.mgz to MNI space so I could overlay results from SPM
and Freesurfer.

I followed some discussions on mailing list and tried this:

mni152reg --s $SUB

mri_label2vol --seg $SUBJECTS_DIR/$SUB/mri/aparc.a2009s+aseg.mgz \
                          --temp /.../spm/spmT_0001.nii \
                          --reg
$SUBJECTS_DIR/$SUB/mri/transforms/reg.mni152.2mm.dat \
                          --o aseg.$SUB.mni152.nii

The process ended without errors, but while watching results in freeview
- the results are not correctly aligned. Is FSL (which is part of
mni152reg procedure) using some other MNI template than SPM?
Any suggestions will be most appreciated.

The freeview snapshot is here:
https://dl.dropboxusercontent.com/u/70539709/Freesurfer_question/freeview_a2009s_mni.PNG


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