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/

Dne 9.9.2016 v 18:53 Douglas Greve napsal(a):

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_a2...

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