What you are trying to do is harder than you think as you are trying to go thru several spaces in several software packages (and using ANALYZE to boot). Why not just use the talairaching in freesurfer?
Wayne Su wrote:
I'm trying to use Flirt from FSL to get talairach.xfm. Here are the steps I took:
- recon-all -autorecon1 -notalairach -subjid $subject
- mri_convert $SUBJECTS_DIR/$subject/mri/nu.mgz
$SUBJECTS_DIR/$subject/mri/nu.img 3) bet $SUBJECTS_DIR/$subject/mri/nu $SUBJECTS_DIR/$subject/mri/nu_brain 4) fsl_rigid_register -i $SUBJECTS_DIR/$subject/mri/nu_brain.img -r $FREESURFER_HOME/average/mni305_brain.cor.mgz -o $SUBJECTS_DIR/$subject/mri/nu_reged.img -dof 12 -cost corratio -xfmmat $SUBJECTS_DIR/$subject/mri/transforms/talairach.xfm
The mni305_brain.cor.mgz is the skull-striped mni305.cor.mgz from average folder. The registered images from flirt is fine. However, when I checked the transform with the tkregister2: tkregister2 --mgz --s $subject --fstal It seems it's a bad transforms. I switched the input and ref volumes in step 4. The result is improved, but still not good. I tried to use orig.mgz instead of nu.mgz, the result is the same. Anything I missed?
Thanks,
Wayne
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