Thanks, this was what we wanted to know. To clarify the whole process, we would still like to briefly confirm something about the second issue (Apologies for our ignorance ;):
It seems that mris_make_template could be the method for making the reference surface for the registration, is this right? If so, is there any options that should be known, or does the method produce the needed properties (mean curvature and convexity) automatically from the curvature files of the given subjects? The information printed using '--help' wasn't too extensive :).
-Janne
-- Janne Hämäläinen Researcher Helsinki University Central Hospital Department of Radiology janne.hamalainen@hus.fi
-----Original Message----- From: Bruce Fischl To: Hämäläinen Janne Cc: 'freesurferÉnmr.mgh.harvard.edu' Sent: 6/7/2004 8:29 PM Subject: Re: ÄFreesurferÅ Properties needed in registration
1. you'll need the ?h.curv (smoothed mean curvature) and ?h.sulc (convexity, generated by mris_inflate) to morph.
2. The ?h.average.tif are multi-frame tif, with 3 sets of 3 frames. Each
set contains mean, variances and dofs for a geometric measure. The 1st set is the curvature of the inflated surface, which is not currently used in
the morph. The second set is convexit (sulc) and the third is the smoothed mean curvature.
cheers, Bruce
On Mon, 7 Jun 2004, Hämäläinen Janne wrote:
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.
- 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?
- 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@hus.fi
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