Hi Fred
we don't have much experience with this. Which synthesis are you using? You might need to use a different one for the talairaching to more closely match the atlas (maybe a TR=20,TE=2.5,flip=20-30 one)
On Mon, 29 Apr 2013, Fred Dick wrote:
Dear all
I'm having difficulties getting correct Talairach.lta's from synthetic flash volumes (Bruce, you are probably sorry you ever told me about this!). Basically the brain is over-scaled (bigger than it should be), which I think is happening because the contrast is so good (gm much darker than wm).
Is there an example of how to use the -flash_parms flag, and what mri_em_register is expecting in the parameter file?
Thanks,
Fred
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer