Sorry, I misinterpreted your question.  In that case, if you want more than the broad-brush description that Bruce provided, you'll likely need to download the source code and scour the c-code yourself to find the exact specifics.

cheers,
-MH

-- 
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mharms@wustl.edu

From: "Caspar M. Schwiedrzik" <cschwiedrz@mail.rockefeller.edu>
Date: Friday, May 31, 2013 2:50 PM
To: "Harms, Michael" <mharms@wustl.edu>, "Freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mprage flag in recon-all

yes, but recon-all just calls mri_segment with -mprage and mri_normalize with -mprage.
I would like to know what -mprage does in these two functions, but i cannot search them because they are executables, not scripts.
Caspar

2013/5/31 Harms, Michael <mharms@wustl.edu>

Use any editor (even Word) with a search capacity, and search for the string 'mprage'.
That will lead to you the variable internal to recon-all called "IsMPRAGE".  Searching for "IsMPRAGE" will then show you all in the stages that the -mprage flag affects.

cheers,
-MH

-- 
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mharms@wustl.edu

From: "Caspar M. Schwiedrzik" <cschwiedrz@mail.rockefeller.edu>
Date: Friday, May 31, 2013 2:14 PM
To: "Freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mprage flag in recon-all

I only find flags for mri_normalize and mri_segment in recon-all, and I have trouble reading the contents mri_normalize with a regular text editor.
caspar


2013/5/31 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Hi Caspar

it changes some parameters to the intensity normalization and segmentation to account for the lower SNR and increased CNR in the mprage. You'll need to look in the recon-all script for the details

cheers
Bruce



On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:

Hi!
Is there more documentation on what settings the mprage flag enables in
recon-all?
Specifically, I would be interested which individual steps it affects and
what  the parameters are for each of the steps.
Thanks!
Caspar





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