You are correct, 3dfim+ does not handle the -input1D option.
It seems to be due to a small oversight in recent changes.
I know little of the operation of the program, but it is quite
likely that fixing the oversight will make it happy again. :)
Since Dr. Cox will not be back until Monday, the AFNI source
distribution will not be updated before then. But I can offer
you an updated 3dfim+.c file for you to compile on your own
system, if you are interested.
Please send me email if you would like the file.
- rick