If this is just a thickness study, then you dont need fsfast. There are
examples/tutorials of this type of analysis in the wiki. Look through
that and see if you still have questions.
doug
Jeff Sadino wrote:
Hello,
I want to run group statistics on the cortical thickness for a study
with 3 groups, each with about 30 subjects. To do this, I need to
create an average cort thickness map for each group. We are
interested in basic statistics, so nothing too advanced. I am
wondering what would be the most efficient way to go about this. From
what I can tell, FsFast is the program used to do group analysis.
Would it be fastest to learn FsFast to process all my group data, or I
am thinking since we only need basic stats, it may be faster and
easier to register each subject's ?h.thickness file to an average
sphere and then load the registered thickness file into matlab to do
the stats? I think I would need to modify the commands from
auto-recon stage 3 to use the thickness file, for example:
mris_sphere ?h.thickness ?h.thickness.sphere
mris_register <http://surfer.nmr.mgh.harvard.edu/fswiki/mris_register>
-curv ?h.sphere
$FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif
?h.thickness.sphere.reg
mris_jacobian <http://surfer.nmr.mgh.harvard.edu/fswiki/mris_jacobian>
?h.white ?h.thickness.sphere.reg ?h.jacobian_white
mrisp_paint <http://surfer.nmr.mgh.harvard.edu/fswiki/mrisp_paint> -a
5 $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#6
?h.thickness.sphere.reg ?h.thickness.avg_curv
We have a cluster, so the processing could be done fairly quickly.
Thank you in advance for your advice!
Jeff Sadino
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