Posted by B. Douglas Ward on April 18, 2002 at 10:59:53:
In Reply to: Re: movie of activations posted by Richard Bargains on April 17, 2002 at 14:25:31:
Hello Richard:
I will assume that you are referring to the same experiment that you descrbed
before, i.e., "My experiment consisted of five 30s blocks with the stimulus on
and five 30s blocks with the control". Question: Is TR = 1 sec?
To make a movie of the response to the "on" stimulus (relative to the control
condition, which might be what you mean by "A-B"), you could do the following:
Create a new input stimulus function. This will be different from the input
stim fn that you used to perform the t-test. This input stim fn will have
a single "1" at the beginning of each "on" block. Again, assuming that
this is the same experiment that you described before, the 1's will
occur at time points 0, 59, 119, 179, 239, and 299; all other time points
will be 0's. Store this as a column into file myStim.1D.
Now, execute the following command line:
3dDeconvolve \
-input func+orig -nfirst 3 -polort 1 -num_stimts 1 \
-stim_file 1 myStim.1D -stim_maxlag 1 44 -stim_label 1 "On" \
-progress 1000 -iresp 1 myResp
The output 3d+time dataset, myResp+orig, will contain, for every voxel,
the "averaged" 45 sec. response to each input "on" block.
1st NOTE: The output is NOT the impulse response function (IRF). Rather, it
is the averaged response to each 30 sec. "on" block.
2nd NOTE: You may notice that in "active" voxels, the response does not
return immediately to baseline at the end of the 30 sec. "on" block (and, the
response does not immediately rise to the max value at the beginning of each
"on" block). This time lag is due to the hemodynamic response. Therefore,
you may wish to use a more subtle statistical analysis than the previously
discussed t-test, in order to determine which voxels are active. For more
details, see the documentation in file 3dDeconvolve.ps.
Doug Ward