Instead of typing the Dimon command to sort datasets, we have created scripts that do this for us. We have used this technique for two of our other studies and it worked fine. We have a script with the following command line:

Dimon -infile_prefix 1 -dicom_org -save_file_list axial -quit

We then have a GERT_Reco script that is an exact copy of an automatically generated GERT_Reco script and has the following:

#!/bin/tcsh

# This script was automatically generated by 'Dimon'.
#
# Please modify the following options for your own evil uses.

set OutlierCheck = '' # use '-skip_outliers' to skip
set OutPrefix = 'OutBrick' # prefix for datasets

to3d -session ../../ -prefix axial \
-time:zt 29 11 1.5sec alt+z \
-@ < axial


But when we try to run this script, we get the following error:
[mamlung@matlab MR]$ source ../../../../GERT_scripts/GERT_Reco_dicom_axial
: command not found
: command not found
: command not found
: command not found
++ Program to3d: AFNI version=AFNI_2006_06_30_1332 [32-bit]
++ Authored by: RW Cox

** NO INPUT IMAGE FILES?

try 'to3d -help'
-bash: -time:zt: command not found
: No such file or directory
: command not found


We havent had this problem before with any of our other datasets. Any ideas?