I am in the process of attempting to learn FSL, and apologize for the lengthy
email. I am using a rapid, event-related design (experimental stimulus timing
and duration were determined by using optseq),FSL 3.2, and the 3 column format
for EV specification.
First, is it necessary to model the control condition? In my first attempt, I
defined each experimental condition and the control condition as an EV, and then
created simple contrasts based on the EVs. That is, I gave one condition a
value of 1, and set all others to zero. I used the default settings for cluster
thresholding (Z thresh=2.3, p<.01), and results indicated significant
activation for approximately 95% of the brain--even for the control condition.
When I attempted to contrast one experimental condition vs the control (as
1,-1), there was absolutely no activation (not surprising considering the amount
of activation in the control condition).
In my second attempt, I did not define the control condition as an EV, and this
resulted in a much more "reasonable" amount of activation for each EV (again
using simple contrast). Is it the case that by not specifying the control
condition that the experimental conditions have been effectively baselined?
Which approach is recommended?
Finally, I am having difficulty viewing the data interactively. Using fslview,
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?
Any suggestions/advice would be greatly appreciated.
Thanks in advance,