Hi,
We are planning to use some of our own methodology (mainly segmentation
routines) in the Freesurfer pipeline to make cortical thickness analysis
between groups. Related to this, there is two things that would need
clarification.
1. In case we would use our own surfaces for analysis, what surface
properties would be needed by the registration software (mris_register) of
Freesurfer, and, more precisely, exactly what curvature files? In the
www-site of Graham Wideman, he presents a data flow chart that tells the
input and output to the number of programs used in the analysis. He has
concluded that the registration would need only the spherical surface file
(rh.sphere or lh.sphere), but that can't be correct, right? Some curvature
information needs to be used, but what? In the article 'High-Resolution
Intersubject Averaging and a Coordinate System for the Cortical Surface'
(HBM 1999) it is said that convexity of the surface can be used. But what is
the property (and curvature file) used in Freesurfer?
2. Then we would of course need our own reference surface for registration,
since we are analysing surfaces constructed differently from the default
Freesurfer surfaces. Is there documentation on what data the reference
surface (e.g. the rh.average.tif or lh.average.tif) contains? Our guess is
that there is curvature data included in this surface file. Is that so, and
is there an easy way to create our own reference surface from a set of
subjects?
Thanks in advance,
Janne Hämäläinen
--
Janne Hämäläinen
Researcher
Helsinki University Central Hospital
Department of Radiology
janne.hamalainen(a)hus.fi