Hi there,
I would like to ask some questions about metric distortion.
1. Following the Wisco et al (2007) paper, metric distortion is defined as
Metric Distortion = k * area of a triangle on a registered sphere / area of triangle on gray/white interface surface
which I believe I can compute using
mris_jacobian $subject/surf/lh.sphere $subject/surf/lh.sphere.reg $subject/surf/lh.sphere.reg.jacobian
The subject 's ?h.sphere.reg is formed from the registration of the inflated sphere of the subject with the Desikan et al. (2006) 40 subject template? From the wiki, I think the command is
mris_register -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.sphere.reg
so the jacobian measure is derived from the parcellation stage (stage3) of recon-all.
2. I would like to extract the k factor for each subject which is defined as
k = total surface area of original gray/white interface surface / total surface area of individual sphere
do I compute this from the total surface area field of
mris_anatomical_stats $subject $hemi orig / mris_anatomical_stats $subject $hemi sphere
or do I need to use outputs from different surfaces or extract either value differently? The sphere values look rather uniform and I wanted to check if I am using the right thing.
3. Finally, I see in the study average make_average_surface.log file:
setting group surface area to be 1142.0 cm^2 (scale=1.29)
and I was wondering what the scale factor represented here.
Thanks in advance for your time.
Cheers,
-Morgan