Maybe waver is the program you want. Also note several of the modeled basis functions in 3dDeconvolve are convolved with a square wave, as described in this excerpt from 3dDeconvolve's help

*** Some models below are described in terms of a simple response
function that is then convolved with a square wave whose
duration is a parameter you give (duration is NOT a parameter
that will be estimated). Read the descriptions below carefully:
not all functions are (or can be) convolved in this way:
* ALWAYS convolved: BLOCK dmBLOCK MION MIONN
* NEVER convolved: TENT CSPLIN POLY SIN EXPR
* OPTIONALLY convolved: GAM SPMGx WAV