The easiest way is to align the brain.mgz to mni152 with flirt, then apply the inverse transform

Nasim Maleki wrote:

Dear all,

I have 3D masks defined in MNI space using FSL. I would like to transform these masks to each subjects anatomical space in FreeSurfer and measure the volumes corresponding to these masks. Should I just count the number of voxels in each mask after transformation to the structural space and report the #voxels x (1x1x1mm3) as the corresponding volume to that mask?

Thanks for your help, Nasim _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer