Hello,

Let me try to clarify some things.

0) What is your TR, and how many time points are there?

1) Are you trying to erode those masks twice? If so, maybe 3dmask_tool would be easier and more direct to use.

2) Do the regressor and regressor_deriv files look like valid time series?

3) Why do you think that the time series were not projected out?

4) Are you attempting to bandpass separate from nuisance regression? This might be part of the problem, in that the output from this will no longer necessarily be orthogonal to the nuisance regressors.

The correct way to do this would be to run 3dDeconvolve using -x1D_stop (i.e. do not actually make an output dataset), just generating the projection matrix X.xmat.1D. Then pass that along with your bandpass options to 3dTproject, so that it can all be part of the same model.

Doing projections in multiple steps has 2 problems:
a. Unless the projection is performed on the second (or later) set of regressors, the second projection will project back in some of what was removed in the first one.
b. Degrees of freedom are not properly accounted for. Bandpassing removes a large fraction of your degrees of freedom, essentially using MANY regressors of no interest. Sometimes just projections would essentially take one to few or even negative remaining DoF.

- rick