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 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! CasparThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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