
"Class Work" (currently starting on slide 9)

All the data and scripts for single subject analysis are under the FT_analysis
directory.  Go there and look at the contents of that directory and of FT.

% cd AFNI_data6/FT_analysis
% ls -l

Scripts s01.ap.simple and s02.ap.align contain afni_proc.py commands for
processing the same data.  The 'simple' script is used in class, while the
more advanced 'align' script is a better example of what to do in general.
The advanced one would take too long to cover in class, but will be covered
to some degree in this tutorial.

Scripts s11.proc.FT and s12.proc.FT.align would come from executing scripts
s01 and s02 (i.e. they are the resulting 'proc' scripts).  They will not be
mentioned again.

The original subject data is under FT (EPI, anat, stim timing).  Looking at
the contents of that directory shows:

------------------------------

% ls -l FT

These are all of the input files to provide to afni_proc.py: the 2 stimulus
timing files, an anatomical dataset and 3 EPI runs.

    AV1_vis.txt, AV2_aud.txt : timing files for the 2 stim classes
    FT_anat+orig/acpc/tlrc   : the anatomical dataset, the acpc and tlrc
                               files can be ignored
    FT_epi_r1/2/3+orig       : the 3 runs of EPI data

------------------------------

Consider the contents of the visual-reliable timing file.

% cat FT/AV1_vis.txt

 60 90 120 180 240
 120 150 180 210 270
 0 60 120 150 240

This shows the stimulus times for the 3 runs (1 row per run).  Each time
is an onset time, in seconds, from the start of the run.  Notice that there
is a stimulus starting at the very beginning of run 3 (time t=0.0 seconds).

Each of these stimuli lasted 20 seconds, which is not encoded in this file.
The duration is encoded in the basis function that we provide to afni_proc.py
(which then appears in the 3dDeconvolve command).  

