Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

[Bruce Fischl]

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:




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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
   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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Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

[Rovai Antonin]

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(Continued)

Of course I meant using the recon-all command!

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

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


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[Hôpital Erasme]

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Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

[Rovai Antonin]

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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 
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:

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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Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

[Bruce Fischl]

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


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[Freesurfer] Reconall with no-MPRAGE T1w image?

[Rovai Antonin]

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
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