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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