I made up some large data (120+ GB) in the form of 250 500 MB datasets, and tried to run 3dDeconvolve on them auto-catenated on the command line. The program was able to read all the data in, set up the regression matrix, and start the work -- but it was taking so long, I killed the job after a while before going to bed.

However, this convinces me that I need more information from you.
The setup of your datasets, as described in my last post.
But also your other inputs - the command line used.
Did you have censoring? Motion regressors? How many stimuli, and of what type?
All I know is that YOUR run failed in the read_input_data() function, which is where all of this stuff is input and organized, so it could be anything that is causing the problem. So I need to know more about all the inputs.