When you use the simple **RegistrationRunner.app** gui it makes a subdirectory in your main registration directory called **commands**.  Whenever you start a new job it saves a ''.command'' file in this directory.  This file contains the actual commandline that is used to invoke the registration software.  There are 3 layers:

  - Registration gui (RegistrationRunner.app, written by Greg)
  - command line wrapper script (munger.pl, written by Greg)
  - core registration tools (registration, warp ..., written by Torsten Rohlfing)

These ''.command'' files call **munger.pl**, which then calls the core tools that actually do the heavy lifting.

You can open these in a text editor to slightly modify the commands, or double click them to re-run the command (a new **Terminal** window will open.

Here is an example.  Note the use of '\' to split long lines.

<code>
#!/bin/sh
# 2008-11-17 19:21:52 GMT
cd "/Volumes/GJ8CHD/JPeople/Sebastian/fruitless/Registration/Job1" \
"/Applications/IGSRegistrationTools/RegistrationRunner.app/Contents/Resources/munger.pl" \ 
-b "/Applications/IGSRegistrationTools/RegistrationRunner.app/Contents/Resources" \
-awr 0102 -v -L -T 2 -s "refbrain/T1.PIC" "images"
</code>

This can be explained as follows:

  * change directory to the required working directory
  * call munger
  * specifying a location for the core registration binaries [-b]
  * run [a]ffine and [w]arp
  * [r]eformat channels 1 and 2
  * be [v]erbose
  * find initial affine transform using [L]andmarks 
  * use 2 threads [-T] (can be up to the same as the number of cores in your machine)
  * -s = reference brain
  * images directory.

Here's another:

<code>
cd "/Volumes/GJ8CHD/JPeople/Sebastian/fruitless/Registration/Job1"
"/Applications/IGSRegistrationTools/RegistrationRunner.app/Contents/Resources/munger.pl" \
-b "/Applications/IGSRegistrationTools/RegistrationRunner.app/Contents/Resources" \
-a -r 01 -l a -s "refbrain/T1.PIC" "images"
</code>

This one:

  * only runs the [a]ffine registration 
  * [r]eformats channel 01 ...
  * and does the reformatting for the [a]ffine registration [l]evel

   
The full command line options for **munger.pl** are:

<code>
Usage: ./munger.pl [OPTIONS] <PICFILE/DIR> [<PICFILE2/DIR2> ...]
Version: 1.17

	-h print this help
	-v verbose (provide extra feed back at runtime)
	-t test run (no commands are actually run)
	-g debug: prints every command run by myexec and the return value
	-p make a scriPt from commands that would be run 
	   (nb cannot produce commands that depend on earlier commands)
	-u statUs - display number of images, registrations etc
	-z turn gzip off (on by default)
	-k lock message ie contents of lock file (defaults to hostname:process id)
	-m maximum time to keep starting registrations (in hours, default 8760=1y)
	   nb this will not stop any running registrations
	-x [never|only|any]:[truncate|delete] Clear input images when done.
	   default is never, eg only:truncate, any:delete
	   only => only the job that runs reformat can clear input
	   any  => any job can delete; in fact a job started with any will not
	           reformat at all. This is useful because you can run a cleanup
               job if it becomes clear that you are running short of space.
	   truncate => leave a 0 length file with same mtime as original image

	-a run affine transform
	-w run warp transform
	-c [01|02|..] channels for registration (default 01 or "")
	-r [01|02|..] run reformat on these channels
	-l [p|a|0..9|f] run reformat on these levels
	   (default f=final warp, p=principal axis, a=affine, 0..9=warp intermediates)
	-f [01|02|..] channel of the images used for registration - default is 01

	[nb use -f to specify the channel of the images that were previously used to
	 generate a registration if you now want to reformat a different channel using
	 that registration information]

	-i register brain to itself if possible (default is to skip)
	-0 Don't output intermediate warp registration levels

	-s [file|fileStem] Reference brain (average e-2 by default)
	-b [path] bin directory
	-d [stem] registration subdirectory (default ./Registration)
	   [nb if this begins in a dot then the value will be appended to both
	   reformatted and Registration directories]
	
	-e File ending of input images (pic, nrrd, nhdr)
	-o File ending of output images (bin, nrrd, nhdr) - defaults to torsten raw bin

	-P find initial affine transform using image principal axes
	-L find initial affine transform using landmarks
	-I inverse consistent warp weight (--ic-weight) default 0, try 1e-5
	-E [energy] energy of warp transform (default e-1)
	-X [exploration] (default 16)
	-M [metric] (default 0 (NMI), options 1=MI)
	-C [coarsest] (default 4)
	-G [grid-spacing] (default 40)
	-R [refine] (default 3)
	-J [0 to 1] jacobian-weight volume constraining param (default 0)
	-T [threads] (default auto)
	
	-A [option] additional options for affine transformation
	-W [option] additional options for warp transformation
  
Munge a BioRad PIC file or (recursively) parse a directory of PIC files
by running the affine and warp registrations and reformatting images
as required.  Final argument must be the images directory or a single image.
</code>