How to create AFNI datasets from multiple runs of data:

There are 4 runs of data stored in these 12 numbered directories.  GE Real Time
pulse sequence stores the runs in this manner (very frustrating and confusing).
As they are stored now, it's difficult to distinguish where one run ends and 
the other one begins.

To fix this problem, run the following "Ifile" command:


   Ifile -nt '*/I.???'

The above command runs the AFNI program Ifile, which uses the internal time
stamp in each image file to determine what run it belongs to.  Ifile will tell
you that we have 4 runs of data stored in these 12 sub-directories.  

Also notice that Ifile will create a script called @GERT_Reco.

Execute this script to create afni briks for these 4 runs of data
(GERT_Reco calls to3d internally, and creates the datasets for you)

To execute the GERT_Reco script, try any one of the following commands:

   ./GERT_Reco
   tcsh GERT_Reco
   source GERT_Reco

For more on Ifile, type Ifile -help

Also read up on Imon, a "sister" program of Ifile (Imon -help).  Imon will
also monitor the images as they are acquired in real time and will tell you if
you have any missing, out-of-sequence, or duplicated images.

There is now a Dicom version of Imon, called Dimon (see Dimon -help)