Hi Kenneth,
If you want to generate an average time series for
voxels in a mask, you can do it using 3dROIstats.
If epi+orig is my 160 time point EPI dataset, and
mask_epi+orig is a mask that I want to apply to it,
then the command:
3dROIstats -mask mask_epi+orig epi+orig
will generate an average value over the mask, for
each sub-brick, i.e. an average time series.
To test it out without having a good mask, you can
generate one on the fly in the 3dROIstats command.
Let's say you want to mask all voxels in sub-brick
zero with a value above 3000.
3dROIstats -mask '3dcalc( -a epi+orig[0] -expr step(a-3000) )' epi+orig
Is this what you are looking for?
- rick
