oh, my mistake. I thought it called them with specific parms. Sorry:
for mri_segment:
gray_hi = 99 ; (same as --ghi 99)
wm_low = 89 ; (same as -wlo 89)
for mri_normalize:
intensity_below = 15 ; (same as -b 15)
cheers
Bruce
On Fri,
31 May 2013, Caspar M. Schwiedrzik wrote:
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 <mha...@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: mha...@wustl.edu
From: "Caspar M. Schwiedrzik" <cschwie...@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 <fis...@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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