Hi AR

1. mprage in general has higher CNR and lower SNR than non inversion-prepared T1w sequences like FLASH. THe -mprage switch takes advantage of this to loosen the intensity gradient threshold in the region filling of the wm.

2. If you just leave out the -mprage switch it will revert to the default behavior

cheers
Bruce



On Tue, 3 Sep 2019, Rovai Antonin wrote:


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Hello,


From the ReconAllTable
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) I see
that the mri_normalize step (producing the T1.mgz file) has the -mprage
option.

I have two questions:
1. What is this option doing exactly? There is no description in the
mri_normalize man page
(https://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize); similarly, the CLI
help doesn’t mention this option.
2. How do I change this when launching a ReconAll without re-writing a custom
pipeline? (For context our T1 is not MPRAGE and we had some segmentation
issues so this is an attempt to debug this).

Thanks for you help

AR

Hôpital Erasme

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