Thanks Rick,

Since it seems that modeling attenuation is a bit difficult (particularly since I don't have a great idea of when or how it would affect the response amplitude), would it be more sensible to focus on duration modulation instead? If so, I can switch the stim_times lines to the following:

-stim_times_IM 1 $data_dir/$s/derivatives/Timing_Files/AM/mut.txt 'dmBLOCK(1)' -stim_label 1 mut \
-stim_times_IM 2 $data_dir/$s/derivatives/Timing_Files/AM/neu.txt 'dmBLOCK(1)' -stim_label 2 neu \

If I do it this way I assume my timing files are now properly formatted.

Regarding the memory mapping,I tried adding this in the command line:
AFNI_NOMMAP=YES ; export AFNI_NOMMAP

before getting this error...

*** MCW_malloc(1301300) from 3dDeconvolve.c#5606 FAILS!
*** current total usage=221187614 bytes
++ current memory malloc-ated = 221,187,614 bytes (about 221 million [mega])
** ERROR: Memory allocation for output sub-bricks fails!
** ERROR: Have allocated 216,015,800 bytes (about 216 million [mega]) for output, up to now
** ERROR: Potential lenitives or palliatives:
++ Use 3dZcutup to cut input dataset into
smaller volumes, then 3dZcat to put
the results datasets back together.
++ Reduce the number of output sub-bricks.
++ Use a system with more memory and/or swap space.
** FATAL ERROR: Alas, 3dDeconvolve cannot continue under these circumstances.
** Program compile date = Feb 5 2018

Am I able to make this change directly in the command line (using bash shell)? I'm using the AFNI version on my university's server, so I don't have permission to alter the .afnirc file.


Dan



Edited 1 time(s). Last edit at 10/04/2018 11:29PM by Dan.