Hi everyone,
while the machine is busy crunching through our data set,
i would
like to prepare myself from the next step of the analysis, which is a
region-wise
analysis of the computed metrics by the freesurfer pipeline. Being a
complete
novice in the use of this software, i would like to know how do i go about
doing the following:
1) With the parcellations already available in freesurfer, i would like to
extract metrics (curvature, lgi, thickness) etc. for each label, and
process them outside freesurfer (matlab, since i am more used to
it). Is it possible to do this within freesurfer or without, i.e read
these
values on the pial/white matter/inflated surfaces, ans also extract
ones
corresponding to a particular label?
2) How do i go about generating a group average of the various maps
that freesurfer generates (curvature/thickness/lgi) ? As i understand,
the analysis is done entirely in the subject space. Can i apply a
transformation
to the generated surfaces for averaging? Or does it require a
re-processing
after registering/reslicing all the data to a common space?
3) I am still struggling with a proper colormap, which can bring out
the structure in out data. I see very nice renderings in various
publications, of data generated with freesurfer. Is it possible to
tweak
the colormap to get such a rendering?
Thanking you all in anticipation,
sid.
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