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Dear Roohi,

The realignment parameters / the rp file would be selected as "Multiple regressors" during model specification.

You can specify your own regressors via "Multiple regressors" or the "Regressors" option, with one value a TR/volume, none of these regressors undergoes convolution. "Conditions" can be left empty in that case. If you want to test for a box-car function you would enter something like 0 0 0 1 1 1 0 0 0 ... . Instead of their binary approach you could also enter values reflecting sine and cosine functions of certain frequencies, downsampled to one value a TR/volume. Something like sin(2*pi*f*(0:(n-1))*TR) entered as "Value" should do it, with f corresponding to the frequency of interest in Hz, n corresponding to the no. of volumes and TR corresponding to the repetition time in s. But please check this yourself.

Alternatively, you can also specify the box-car functions via onsets and durations, but then you have to turn off the convolution. https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;fbddcce4.1009 is an old thread on that topic and Guillaume provides a solution, but the code seems to have been changed since then. @ Guillaume / other SPM authors: Maybe we could get a "No convolution" option for the GUI with the next update? Or maybe it's already hidden somewhere?

Hope this helps for the moment,

Helmut