-mprage is probably your best bet, but it would be worth trying out both
ways and seeing the differences.
On Thu, 21 Mar 2013, Garikoitz Lerma-Usabiaga wrote:
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 <ni...@nmr.mgh.harvard.edu>
wrote:
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?
>
> Thanks
> Josh
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