Dear Bruce et al,
could you please confirm the following is reasonable?
I am trying to register "whole brain" surfaces across subjects, hence
creating a study specific template (if anyone is interested in the template,
let me know).
First, run the following to create an individual subject (C01) template:
mris_make_template rh sphere c01
/usr/local/freesurfer/average/rh.wholebrain.tif
Are any other arguments required? This command, as above, creates the
output file only, no other files like those in the
/usr/local/freesurfer/average/ area are created. What are the *.gcs or
tissue_parms.txt files? The .tif is not a graphics file - what does tif
stand for? The rh.wholebrain.tif is the same size as other template files,
so that should be a good sign that it contains the required data.
Then, after spherical transforms for all subjects, the rh.sphere surfaces
are registered to this individual subject template, using a csh script
containing:
set avg="/usr/local/freesurfer/average/rh.wholebrain.tif"
mris_register -curv -w 0 ${sub}/surf/rh.sphere $avg
${sub}/surf/rh.sphere.reg
What are the -curv and -w options and how do they affect the registration?
That completes the first pass of the registration process. Then create a
new wholebrain template, using all subjects' sphere.reg files:
set sub="c01 c02 c03 c04 c05 c06 c07 c08 c09 c10 p02 p04 p05 p06 p07 p08
p09"
mris_make_template rh sphere.reg $sub
/usr/local/freesurfer/average/rh.wholebrain.tif
This should create a template that is the average of all these subjects.
Then the registration process is repeated to overwrite the sphere.reg files
for each subject, using the new averaged template.
Is this reasonable? If it has worked correctly, it should now be possible
to use mris_surfglm on the rh.sphere.reg files.
Thanks, Darren
--
Darren Weber, PhD Student
Cognitive Neuroscience, School of Psychology
Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust.
Ph: (61 8) 8201 3889, Fax: (61 8) 8201 3877
http://203.3.164.46/~dlw/homepages/index.html
