Converting dicom files to a single minc file.

For data acquired on the Siemens Magnetom Vision 1.5 (i.e., before
March 22, 2002).  Definitely works if all dicom files are part of one
run (e.g., anatomic data).  Not so sure if this works when files in
the dicom directory are for many runs... And, furthermore, the images
generated by this script cause do_mritotal to barf!

Vanilla combo:

$> dicom_to_minc /output/directory -inputdir /input/directory

---- The Help File ----
shadow:PET/mri> dicom_to_minc -h

Dicom-specific options:
-big_endian_image:     Specify that the image is big endian

Command-specific options:
-list:                 Specify a file for listing contents of tape
-tape:                 Specify an input tape drive
		       (default=/dev/nrtape if no files given)
-notape:               Do not try to use the tape drive
-inputdir:             Specify directory from which input file names
		       should be read 
-nominc:               Do not produce output minc files
-first:                Specify a starting tape position (#files to
		       skip) 
-last:                 Specify an ending tape position
-compress:             Compress the output minc files
-nocompress:           Do not compress the output minc files (default)
-ignore_image_errors:  Ignore errors when reading images 

Generic options for all commands:
-help:                 Print summary of comand-line options and abort

Usage: dicom_to_minc <outputdir> [<file1> <file2> ...] [<options>]       
-------------------------



For data acquired on the Siemens Sonata 1.5 (i.e., after ~April 15,
2002).  This will parse all files in the dicom directory, assign
them to the proper run and generate the appropriate .mnc file.  You
must specify a directory other than the one where the dicom files live.

Vanilla combo:

$> /software/build/external/dcm2mnc /scratch/kate/dicomfiles/*  /scratch/kate/subjectdir 

---- The Help File ----
shadow:kate/dicomfiles> /home/bic/rhoge/bin/dcm2mnc -help
 
Usage:  dcm2mnc [options] file1 file2 file3 ... destdir
 
options:
  -help           : print this informative message
  -list           : print list of series (don't create files)
  -anon           : exclude subject name from file header
  -descr <str>    : use str as session descriptor (default = patient initials)
  -idstr <str>    : use str as subject id string (default = patient ID)
  -log <0|1|2|3>  : set logging level (default=0)
  -cleanup        : delete input files when done (careful!)
  -cmd <prog>     : apply prog to output files (e.g. gzip)
  -fork           : fork subprocesses to create minc files (now default)
  -nofork         : don't fork subprocs, do show progress for individual files
  -debug          : print debugging info
 
Files are named according to the following convention:
 
  Directory:  descr-idstr-scanner-serialno-date-time/
  Files:      descr-idstr-scanner-serialno-date-time-series-modality.mnc     

See also http://www.bic.mni.mcgill.ca/users/mferre/dcm2mnc_help.html