Yes, I did set the slice timing as you mentioned- "alt-asc".  This is the matlab echo line:

matlab -nodesktop -nosplash -r addpath /Users/PowerPC/pestica_afni_v1_3; [card,resp]=apply_PESTICA2(15,'131A_ep2d.moco+orig','131A_ep2d.moco.brain+orig','alt-asc'); fp=fopen('card_rawest.dat','w'); fprintf(fp,'%g\n',card); fclose(fp); fp=fopen('resp_rawest.dat','w'); fprintf(fp,'%g\n',resp); fclose(fp)

I'm using Version 1.3 (including the v1.4 update) so that it will jive with my version of AFNI.

Here is the full error message:

> In path at 110
In addpath at 87
In apply_PESTICA2 at 35
??? Index exceeds matrix dimensions.

Error in ==> apply_PESTICA2 at 68
load(sprintf('Volumes/Einstein/PestICA/131A_ep2d.moco_pestica/pestica_%dcomps_slice%d.mat',ep2d_filename(1:end-5),comps,zstart(1)),'A');