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(Continued)

Of course I meant using the recon-all command!

On 3 Sep 2019, at 15:48, Rovai Antonin 
<antonin.ro...@erasme.ulb.ac.be<mailto:antonin.ro...@erasme.ulb.ac.be>> wrote:


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Hi Bruce,

Thanks for your response. From what I read on the wiki 
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) the switch 
in on by default since freesurfer6.0 (but that doesn’t seem to be the case in 
5.3).
At any rate we use the BRAVO sequence (on a GE MRI) and it also has an 
inversion pulse (also CNR isn’t as good as in a MPRAGE).

Best

Antonin

On 3 Sep 2019, at 15:44, Bruce Fischl 
<fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>> wrote:

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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