The current version of Freesurfer calculates numerous curvature-based
functions by default in the recon stream. If you look in the "surf"
directory for a reconstructed surface, you'll see several "curvature"
files that end in "*.crv".
By default, these are created for the gray/white junction surface (the
*smoothwm* implies the smoothed white matter surface). The functions
are all derived from the principal 'k1' and 'k2' curvatures that are
calculated at each vertex point on the surface mesh, and are defined as
k1 maximum curvature
k2 minimum curvature
K Gaussian = k1*k2
H Mean = 0.5*(k1+k2)
C Curvedness = sqrt(0.5*(k1*k1+k2*k2))
S Sharpness = (k1 - k2)^2
BE Bending Energy = k1*k1 + k2*k2
SI Shape Index = atan((k1+k2)/(k2-k1))
FI Folding Index = |k1|*(|k1| - |k2|)
The lh.curv and rh.curv files that are somewhat smoothed versions of
the 'H' mean curvature, thus lh.curv is not equal to
lh.smoothwm.H.crv, but close. Also, the lh.curv/rh.curv are calculated
using a different algorithm than the curvature values for the above.
The main curvature calculating process is 'mris_curvature_stats'. If
you want to generate all the curvature functions for the pial surface,
you might try:
$>mris_curvature_stats --writeCurvatureFiles -G -F pial $SUBJECT $HEMI
where you should replace the "$SUBJET" with your subject, and "$HEMI"
with either 'lh' or 'rh' for the hemisphere. When you run the command,
your terminal will also report the results of several integral
functions taken across the whole curvature function surface, and will
also report the 'Folding Index', and several Intrinsic Curvature
Indices: the positive (ICIp), negative (ICIn) and natural (INIn). The
natural Intrinsic Curvature should be close to 1.0000 by definition.
For more information, I suggest you read the help/man page for
'mris_curvature_stats':
$>mris_curvature_stats -u | more
Zhangyuanchao wrote:
Dear Mr or Ms
Is there any way that we can obtain curvature value of the pial surface?
I am not sure whether lh.curv is the curvature file that I want. How can
I calculate the mean curvature, Gauss curvature of the pial surface and
the GM/WM interface?
Is there any built-in function in freesurfer to calculate the above index?
Is there any other measures of cortical foldings in freesurfer besides
lGI and curvature?
Thanks a lot!
yczhang
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Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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