Dear Scott,

Your email raises a couple of issues.  First, wrt to modeling a control
condition -- if you also have sufficient "null events", then you probably
do want to model your control events because otherwise the two will be
conflated.  If you didn't include null events, you probably don't want to
model the control condition because it will presumably result in a rank
deficient design matrix.  This choice will determine how to do your
contrasts.  If you model all conditions (rank deficient case), then each of
your contrasts must add to zero (ie not [0 1]) because there is no implicit
baseline for comparing EV2 to.  This can easily lead to whole brain
activation because the contrast itself isn't meaningful.  Finally, when you
compare activation to control conditions (ie [1 -1]) and don't see any
activation, this most likely reflects choosing an inappropriate statistical
threshold.  The default of cluster stats (Z>2.3, p<0.01) is very
conservative in that it requires literally hundreds to thousands of
contiguous voxels to show any activation as significant.  This has come up
many times on this list so it may be worth looking through the archives for
more details.

>Finally, I am having difficulty viewing the data interactively.  Using
>I can open thresh_zstat1 and overlay the data on example_func.hdr.  However, I
>would like to view the activation overlaid on the subjects high resolution
>anatomical and the MNI brain (which were used during registation as the main
>structural image and the standard space image respectively).  I have tried to
>view the functional data on highres.hdr,standard.hdr, and the
>avgt152_brain.hdr, but have received the "cannot load incompatible overlay"
>error message.  Is there a way to load the transformation files in fslview?

Using flirt, transform the zstat images you're interested in into either
the subject's high res structural space or into standard (MNI) space and
then overlay the transformed images onto the appropriate image.

Hope this helps.


Joseph T. Devlin, Ph. D.
FMRIB Centre, Dept. of Clinical Neurology
University of Oxford
John Radcliffe Hospital
Headley Way, Headington
Oxford OX3 9DU
Phone: 01865 222 494
Email:  [log in to unmask]