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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 <fischl@nmr.mgh.harvard.edumailto:fischl@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 Hôpital Erasme Lien vers Disclaimer

[Hôpital Erasme]

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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
  <fischl@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
  Hôpital Erasme
  Lien vers Disclaimer

Hôpital Erasme

Lien vers Disclaimer

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