When
would you prefer masked contrast images over traditional
SPM t-maps?
It depends on what you want. If you are
interested to locate a biologic effect as precise as
possible, I'd prefer masked contrast images since they are
independent of the amount of local noise. Local noise
comprises many components from measurement error to
biologic variance deriving from other neurons that can be
found in the same brain region but serve other purposes.
Why divide by those if you are not interested in them?
On the other side, you may be interested in regions to be
used in a second analysis. In a PET study, e.g., you may
search for brain regions that differ between patients and
controls and use these regions to create a diagnostic index
in further patients. Or you may identify brain regions with
a significant group difference (e.g. patients versus
controls) and extract data from these regions for
correlation analysis in one group (e.g. disease severity,
disease duration etc.). In that case you probably prefer
the original t-map clusters, since you are interested in a
region with a good signal-to-noise ratio.
At least, you should at least try out mascoi, so you get a
feeling for what you have been missing so far ;-)
I am getting the error message sorry,
only traditional voxel sizes (multiples of .5mm) are
supported
I'm sorry for this. I started mascoi by
copying and pasting some matlab routines I've been using
for quite some time. The algorithm by which the sections
are created is one of them. It is not incredibly flexible,
but I like the image quality it produces. I know, I could
use one of SPM's routines to become resolution independent,
but I do not have very much time for coding at the moment.
What can you do if you get this message? You can still use
mascoi for its basic functionality, i.e., obtain a list of
suprathreshold clusters, see the stats that describe how
"masked contrast images" differ from the original clusters,
select a subset that will be displayed in colored maximum
intensity projections and export the 3D masked contrast
volume. However, to generate sections, you'll have to
browse the created volume with an external
viewer.