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 >>> >>> >>> >>> >> >> The 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<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. >> > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. >
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