While we don't have access to de source code it would be interesting that most of the "tunning" keys are documented.
-----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Don Hagler Sent: segunda-feira, 17 de setembro de 2007 04:01 To: [EMAIL PROTECTED] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness and curvature I looked at the code and found another option for mris_thickness: -N for neighborhood size. For mris_make_surfaces, the default is 20, but for mris_thickness, the default is 2. So setting it to 20 gave the correct result. >From: "Don Hagler" <[EMAIL PROTECTED]> >To: [EMAIL PROTECTED] >CC: freesurfer@nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] thickness and curvature >Date: Sun, 16 Sep 2007 23:23:50 -0700 > >Hi Bruce, > >Thanks for the info. > >mris_curvature gave me identical results as mris_make_surfaces with 10 >smoothing steps. > >mris_thickness gave slightly different values compared to >mris_make_surfaces. Many vertices were identical, but many were not and >some were off by as much as 0.2 mm. > >Is there any reason to think that mris_make_surfaces and mris_thickness >would have differences in how the thickness measurements are done? I'm >doing this with version 3.0.2 at present. > >Don > > >>From: Bruce Fischl <[EMAIL PROTECTED]> >>To: Don Hagler <[EMAIL PROTECTED]> >>CC: freesurfer@nmr.mgh.harvard.edu >>Subject: Re: [Freesurfer] thickness and curvature >>Date: Sun, 16 Sep 2007 20:44:11 -0400 (EDT) >> >>Hi Don, >> >>I just added some help to these utilities: >> >>./mris_curvature >>usage: ./mris_curvature [options] <input surface file> >> >>This program will compute the second fundamental form of a cortical >>surface. >>It will create two new files <hemi>.<surface>.H and <hemi>.<surface>.K >>with the >>mean and Gaussian curvature respectively. >>valid options are: >> >> -w save curvature files (will only generate screen >>output without this option) >> -max save 1st (max) principal curvature in >>?h.<surface>.max file >> -min save 2nd (min) principal curvature in >>?h.<surface>.min file >> -a <avgs> perform <avgs> iterative averages of curvature >>measure before saving >> >> >> ./mris_thickness >>usage: ./mris_thickness [options] <subject name> <hemi> <thickness file> >> >>This program measures the thickness of the cortical surface and >>writes the resulting scalar field into a 'curvature' file <thickness >>file>. >> >>valid options are: >> >>-max <max> use <max> to threshold thickness (default=5mm) >> >> >>is there anything else you need? This will be in the next release. >> >>Bruce >>On Sun, 16 Sep 2007, Don Hagler wrote: >> >>>I see that mris_make_surfaces is normally used to generate thickness and >>>curvature. I would like to generate the ?h.thickness and ?h.curv files >>>without running mris_make_surfaces (I already have white and pial >>>surfaces). >>> >>>Can mris_thickness and mris_curvature (or other programs) give the same >>>results? Those two programs are not heavily documented, so any help on >>>which options to use (to give the same results as mris_make_surfaces) >>>would be appreciated. >>> >>>_________________________________________________________________ >>>Kick back and relax with hot games and cool activities at the Messenger >>>Café. http://www.cafemessenger.com?ocid=TXT_TAGHM_SeptHMtagline1 >>>_______________________________________________ >>>Freesurfer mailing list >>>Freesurfer@nmr.mgh.harvard.edu >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> > >_________________________________________________________________ >A place for moms to take a break! >http://www.reallivemoms.com?ocid=TXT_TAGHM&loc=us >_______________________________________________ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _________________________________________________________________ A place for moms to take a break! http://www.reallivemoms.com?ocid=TXT_TAGHM&loc=us _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
