Briefly: Why Batch Script

1
Briefly Why Batch Script?

• In the Keck Lab

2
Overview

• Computing issues with fMRI processing
• Reasons we need a better way.
• Why batch scripting is that way.

3
fMRI Processing

• For Each Subject

Functional Data
Slice Time Correction (1)
Motion Correction (2)
Anatomical Data
Standardizing Space (3)
Individual Statistics
Group Statistical Maps
Group Statistics (N)
4
fMRI Processing from a computing perspective.

• For Each Subject

Input Data (1)
Process (1)
Process (2)
Input Data (2)
Process (3)

Final Data
Process (N)
5
Realities of fMRI processing

• Each process can take a significant amount of
  time.
• There are many different ways to run a single
  process.
• The analysis must be specific to the study.

Process (1 min)
Process (15 min)
Process (4 min)
Process (45 min)
Processing Time 65min (For Each Subject!)
6
Issues with command line processing.

• Long Commands (i.e. to3d command in AFNI)
• Some commands have syntax that is difficult to
  remember.
• Typing/syntax errors.
• I dont want to sit and wait!

7
What is Batch Scripting?

• Batch Scripting is a term used to describe a
  program or set of commands that will execute as
  many commands without user interaction.

8
Batch Benefits

• Multiple commands can be run via one interaction
  with the computer.
• Programs can continue even when you log out.
• (Visit the keck-help web-site for instructions as
  to how this is done.)
• An interface can be created that will manage
  command-line syntax for you.

9
How do I Batch Script?

• Learn to program.
• Use someone elses scripts.
• Here is where I turn it over to Tom.