munger.pl help

mungerhelp.txt

Usage: /usr/local/bin/munger [OPTIONS] <PICFILE/DIR> [<PICFILE2/DIR2> ...]
Version: 1.21

	A wrapper script for CMTK registration software. For more on CMTK see:
	  http://www.nitrc.org/projects/cmtk/

	-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]
	-F Read path to input files, one per line, from <PICFILE1> ...
	   NB path should be absolute or relative to registration directory e.g.
	     images/imagea-01.nrrd
	     images/imageb-01.nrrd

	-e File ending of input images (pic, nrrd, nhdr)
	-o File ending of output images (bin, nrrd, nhdr) - defaults to nrrd

	-H use Amira's Generalised Hough Transform to initialise affine registration when available
	   (nb the registration folder should be called Registration/affine/XXX_ght.list)
	-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] (Supported values: nmi, mi, cr, msd, ncc, default is nmi)
       See warp --help for details
	-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
	-1 use this brain for reformatx target
	-2 [option] additional options for reformatx
  
Munge a BioRad PIC or nrrd file or (recursively) parse a directory of PIC/nrrd
files by running CMTK affine and warp registrations and reformatting images
as required.  Final argument must be the images directory or a single image.