oh, I see. Yes it is defaulted to being on in recon-all. You can specify -no-mprage to recon-all to turn it off, although it might be worth trying both out on a set of subjects and seeing which does a better job

cheers
Bruce

On Tue, 3 Sep 2019, Rovai Antonin wrote:


        External Email - Use Caution        

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> 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:

              External Email - Use Caution        
      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
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