Well, I had 128 mb ram, and I just doubled it to 256, but I'm still having the same trouble. I can see all 256 mb when I run the free command, though I may still need more. This is just a testing box, and I could probably set this all up on a newer machine. Maybe these error messages will give you a better idea:

This is what happens when I try to run the script with one of the two templates that crash. Both of these templates are the ones that give the "can't find anat parent" warning. (see below)

fmriuser@osiris-l:~/Desktop/Auto Talairach Test Folder$ @auto_tlrc -base TT_icbm452+tlrc -input AT_TEST_ns+orig -no_ss
Parsing ...
Using template from /home/fmriuser/abin ...
++ Program 3dinfo: AFNI version=AFNI_2005_10_31_1510 [32-bit]
++ Program 3dinfo: AFNI version=AFNI_2005_10_31_1510 [32-bit]
Center distance of 18.521933 mm
Padding ...
++ Program 3dZeropad: AFNI version=AFNI_2005_10_31_1510 [32-bit]
++ output dataset: ./__ats_tmp___AT_TEST_ns_ref_TT_icbm452_40pad+tlrc.BRIK
Resampling ...
++ Program 3dcalc: AFNI version=AFNI_2005_10_31_1510 [32-bit]
++ Program 3dcalc: AFNI version=AFNI_2005_10_31_1510 [32-bit]
Clipping -0.000100 6856.000100 ...
++ Program 3dcalc: AFNI version=AFNI_2005_10_31_1510 [32-bit]
++ Program 3drefit: AFNI version=AFNI_2005_10_31_1510 [32-bit]
++ Processing AFNI dataset ./AT_TEST_ns_rs+tlrc.HEAD
++ Changed dataset view type and filenames.
++ Program 3drefit: AFNI version=AFNI_2005_10_31_1510 [32-bit]
++ Processing AFNI dataset __ats_tmp___AT_TEST_ns_resamp_NN+tlrc.HEAD
++ Changed dataset view type and filenames.
++ Program 3drefit: AFNI version=AFNI_2005_10_31_1510 [32-bit]
++ Processing AFNI dataset __ats_tmp___AT_TEST_ns_resamp_edge_art+tlrc.HEAD
++ Changed dataset view type and filenames.
Registration (quintic final interpolation) ...
++ Program 3dWarpDrive: AFNI version=AFNI_2005_10_31_1510 [32-bit]
malloc failure for image space: 94249168 bytes
in file: mri_new.c at line 176
mri_new_7D_generic
mri_warp3D_align_setup
3dWarpDrive main
Error: Failed in 3dWarpDrive
fmriuser@osiris-l:~/Desktop/Auto Talairach Test Folder$

Here's the full version of the warnings I get when I run afni in the afni home directory.

GPL AFNI: Analysis of Functional NeuroImages, by RW Cox (rwcox@nih.gov)
This is Version AFNI_2005_10_31_1510
[[Precompiled binary linux_glibc22: Nov 9 2005]]

** This software was designed to be used only for research purposes. **
** Clinical uses are not recommended, and have never been evaluated. **
** This software comes with no warranties of any kind whatsoever, **
** and may not be useful for anything. Use it at your own risk! **
** If these terms are not acceptable, you aren't allowed to use AFNI.**
** See 'Define Datamode->Misc->License Info' for more details. **

Thanks go to A Clark for great efforts

Initializing: X11.. Widgets...... Input files:
session # 1 = /home/fmriuser/abin/ ==> 4 datasets
dataset count = 4
Time series = 0 files read
** Can't find anat parent PPC_ORgtdWt9YsZTUKhSEC2B6g of /home/fmriuser/abin/TT_N27+tlrc.HEAD
** Can't find anat parent RWC_HZ6leNMfKwp10iTTg78zaA of /home/fmriuser/abin/TT_icbm452+tlrc.HEAD
NLfit & NLerr= Found 16 models
Plugins = 48 libraries read
-orient = RAI

Sorry to keep bugging you about this, but hopefully this information will help others at some point.