Hi Rick,
Thanks, I included the motion parameters using columns 1-6 from the output of -1dfile and the script works now. I am also using now in my 3dDeconvolve script the -iresp option.
Sorry if it was not clear, but my other question in the previous message was what sub-bricks do I use for each subject if I want to run t-tests comparing for example two groups on one condition. Since I have 7 timepoints do I use all of them and use the bucket file for my t-tests, or do I use one time point, or is the output of the -iresp file to be used? hope this makes more sense.
Thanks a lot,
Alessandra