Hi Bruce
I'm using TR=20, flip=30, TE=5 - but possibly irrelevant as also have the -w flag on.
I originally thought this was from a bad brainmask, but then generated a good one and same thing happening.
On 29 Apr 2013, at 14:27, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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
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