Regarding the -mprage tag, we read in the recon-all help that:
-mprage : assume scan parameters are MGH MP-RAGE protocol -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol. both mprage flags affect mri_normalize and mri_segment, and assumes a darker gm
Would you recommend using -mprage for any MP-RAGE or just if you use the same protocol by Andre (that appears in the fs wiki and his website) ?
We are using a standard MP-RAGE sequence (not multiecho) with very similar parameters to the ones recommended by Andre, but not exactly the same.
Many thanks!, Gari
On Thu, Mar 7, 2013 at 1:54 AM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
Josh,
The new -3T flag affects the nu correction stage, and specifies a 3T-based target for the talairach alignment, and the existing -mprage flag affects mri_normalize and mri_segment, so you can use both.
Nick
The new Freesurfer has an optional flag to adjust NU intensity correction parameters for images acquired on 3T scanners. There exists also a flag for MPRage sequences.
I use 3T MPRages. What is the recommended use in this case?
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