Hi!

Thank you very much for replying and sorry for the late reply. I had thought no one could answer.

3dDeconvolve -input m1.nii -nfirst 0 -polort 0 -mask brain_mask.nii \
-fitts fit_m1.nii -errts residual_m1.nii -num_stimts 1 -stim_file 1 $stim -stim_label 1 Visual -x1D X_m1.1D -xjpeg X_m1.jpg \
-tout -bucket stats_m1.nii.gz;

Here is what I run with a representative mouse 1 dataset inputted. This is a spatially template registered image. I pre-detrend hence why I use polort 0. (I understand detrending here is better, but I found it to have negligible effect on mouse data).

The stim file is a 1D file of 0 baseline with the shape of the model represented from a range of 0-1. We've tried other model methods in 3dDeconvolve, but the rodent HRF shape is vastly different from humans that no model worked well from what I've tried.

The output from this mouse results in 1 and 0.135185. It seems the mean of the regressors is not 0?

Thank you for your help