Hi Alice

I believe that the best way to go about this is to use the -CENSORTR option to 3dDeconvolve:

[-CENSORTR clist] clist = list of strings that specify time indexes
to be removed from the analysis. Each string is
of one of the following forms:
37 => remove global time index #37
2:37 => remove time index #37 in run #2
37..47 => remove global time indexes #37-47
37-47 => same as above
2:37..47 => remove time indexes #37-47 in run #2
*:0-2 => remove time indexes #0-2 in all runs
+Time indexes within each run start at 0.
+Run indexes start at 1 (just be to confusing).
+Multiple -CENSORTR options may be used, or
multiple -CENSORTR strings can be given at
once, separated by spaces or commas.
+N.B.: 2:37,47 means index #37 in run #2 and
global time index 47; it does NOT mean
index #37 in run #2 AND index #47 in run #2.

Doing this means you do not have to change your timing files. If you wanted to remove those time points altogether, something like

3dTcat -prefix removed "your_file+orig[0-36,43-(end)] would work, but then you would need to change the timing

Also, I think perhaps $ could be substituted for end there, AFNI can be tricky!

JK