Jim,
Thanks for your input on how to use 3dmaskave. I actually took Bob's advice and applied a mask using the 'Draw Dataset' plugin. All the voxels I was interested in were specified as 1, and those I wasn't interested in were specified as 0.
Unfortunately, I'm a little confused about the output of the timeseries text file. I have 145 TR's that I was hoping to average with all the voxels within the mask. So, my expectations were that if I used 3dmaskave, it would output 145 timepoints that were a representation of the complete timecourse of the response within my roi. The timeseries.txt file that I got, on the other hand, only output 40 points. Is there a reason for this? Maybe I just don't understand what the 3dmaskave is doing, so if you can give a little more explanation that would be useful.
My command line was the following:
3dmaskave -quiet -mask roi_mask+orig \
realigned_&_filtered_functionals+orig > timeseries.txt
So, the differences I can see are that I didn't apply the -mindex because everytime I tried it told me the "-mindex value is too large!" (I used -mindex 1 1). Also, I used my original dataset that had no reference function or statistics applied too it. It was just the raw functional dataset. Did one of my changes cause the mix up, or again, do I just not understand what the function of 3dmaskave is. Please help clarify. I appreciate it.
David
