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" dhaglerjr@hotmail.com To: fischl@nmr.mgh.harvard.edu 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 fischl@nmr.mgh.harvard.edu To: Don Hagler dhaglerjr@hotmail.com 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 screenoutput 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.
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