Posted by Phoebe on March 18, 2001 at 16:01:43:
In Reply to: Re: 3dDeconvolve for t-test posted by B. Douglas Ward on March 15, 2001 at 16:02:01:
I still got some problem in producing a mask. I use the following 3dcalc command with my original 3d+time dataset (bold+orig) to create a mask.
3dcalc -a bold+orig -b bold+orig -expr 'step(b-100)*a' -prefix bold_mask
then put the mask in the 3dDeconvolve for t-test as follows:
3dDeconvolve -input bold+orig -nfirst 20 -nlast 139 -polort 1 -mask 'bold_mask+orig[0]' -num_stimts 1 -stim_file 1 para.1D -stim_label 1 "para" -fout -rout -tout -bucket bold.buck
However, the functional overlay doesn't clear up much for the noises outside the brain. Did I miss something? or just simply increase using a larger number instead of 100?
Where can I get the rough idea of the intensity value to be cleared up?
Many thanks.
Phoebe.