--- a/progs/mincpik/mincpik
+++ b/progs/mincpik/mincpik
@@ -14,7 +14,8 @@
 
 use strict;
 use warnings "all";
-use Getopt::Tabular;
+use Getopt::Long;
+use Pod::Usage;
 use File::Basename;
 use File::Temp qw/ tempdir /;
 
@@ -30,11 +31,12 @@
 
 $me = &basename($0);
 %opt = (
+   'help' => 0,
+   'man' => 0,
    'verbose' => 0,
    'clobber' => 0,
    'fake' => 0,
    
-   'slice' => undef,
    'scale' => 2,
    'width' => undef,
    'bitdepth' => 8,
@@ -42,6 +44,8 @@
    'image_range' => undef,
    'auto_range' => 0,
    'lookup' => undef,
+   
+   'slice' => undef,
    'dirs' => ['zspace'],
    
    'triplanar' => 0,
@@ -55,113 +59,54 @@
    'anot_bar' => undef,
    );
 
-$Help = <<HELP;
-| $me generates image files from MINC volumes using the Imagemagick
-|    convert utility. For a complete list of output file types see the
-|    convert man pages. (man convert) The resulting image is piped to
-|    STDOUT
-|
-| EXAMPLES:
-| To display a default view, transverse slicing, middle slice
-| using display. (display is part of the Imagemagick package)
-|
-|    \$ mincpik infile.mnc PNG:- | display -
-|
-| To generate a PNG file of the 15th coronal slice
-|
-|    \$ mincpik -slice 15 -coronal infile.mnc outfile.png
-|
-| To generate a JPG file using the hotmetal lookup table
-|    with the image range 0 to 100
-|
-|    \$ mincpik -lookup '-hotmetal' -image_range 0 100 infile.mnc outfile.jpg
-|
-| ImageMagick:  http://www.wizards.dupont.com/cristy/ImageMagick.html
-|    NB: ImageMagick should be compiled without 16-bit quanta.
-|
-| Problems or comments should be sent to: a.janke\@gmail.com
-HELP
-
-$Usage = "Usage: $me [options] <infile.mnc> [<image.type>]\n".
-         "       $me -help to list options\n\n";
+# Check arguments
+&GetOptions(
+   'help|?' => \$opt{'help'},
+   'man' => \$opt{'man'},
+   'version' => sub { &print_version_info },
+   'v|verbose' => \$opt{'verbose'},
+   'c|clobber' => \$opt{'clobber'},
+   'f|fake' => \$opt{'fake'},
+   
+   'scale=i' => \$opt{'scale'},
+   'width=i' => \$opt{'width'},
+   'depth=i' => \$opt{'bitdepth'},
+   
+   'title' => \$opt{'title'},
+   'title_text=s' => \$opt{'title_text'},
+   'title_size=i' => \$opt{'title_size'},
+   'anot_bar=s' => \$opt{'anot_bar'},
+   
+   # Image range and lookup table options
+   'range=f{2}' => \@{$opt{'range'}},
+   'image_range=f{2}' => \@{$opt{'image_range'}},
+   'auto_range' => \$opt{'auto_range'},
+   'lookup=s' => \$opt{'lookup'},
+   
+   # Slicing options
+   's|slice=i' => \$opt{'slice'},
+   'z|axial|transverse' => sub { $opt{'dirs'} = ['zspace']; },
+   'y|coronal' => sub { $opt{'dirs'} = ['yspace']; },
+   'x|sagittal' => sub { $opt{'dirs'} = ['xspace']; },
+   
+   # triplanar options
+   't|triplanar' => \$opt{'triplanar'},
+   'tilesize=i' => \$opt{'tilesize'},
+   'sagittal_offset=i' => \$opt{'sagittal_offset'},
+   'sagittal_offset_perc=i' => \$opt{'sagittal_offset_perc'},
+   'vertical' => \$opt{'orientation'},
+   'horizontal' => \$opt{'orientation'},
+   ) or pod2usage(-verbose => 1) && exit;
 
-@opt_table = (
-   ['-verbose', 'boolean', 0, \$opt{'verbose'},
-      'be verbose'],
-   ['-clobber', 'boolean', 0, \$opt{'clobber'},
-      'overwrite existing files'],
-   ['-fake', 'boolean', 0, \$opt{'fake'},
-      'do a dry run, (echo cmds only)' ],
-   ['-slice', 'integer', 1, \$opt{'slice'},
-      'slice number to get',
-      '<int>'],
-   ['-scale', 'integer', 1, \$opt{'scale'},
-      'scaling factor for resulting image',
-      '<int>'],
-   ['-width', 'integer', 1, \$opt{'width'},
-      'autoscale the image to have a fixed image width (in pixels)',
-      '<int>'],
-   ['-depth', 'integer', 1, \$opt{'bitdepth'},
-      'bitdepth for resulting image 8 or 16 (MSB machines only!)',
-      '<int>'],
-   ['-title', "boolean", 0, \$opt{'title'},
-      "add a title to the resulting image"],
-   ['-title_text', "string", 1, \$opt{'title_text'},
-      "use <string> for the title [default: input-filename]",
-      "<string>"],
-   ['-title_size', "integer", 1, \$opt{'title_size'},
-      "font point size for the title",
-      "<int>"],
-   ['-anot_bar', "string", 1, \$opt{'anot_bar'},
-      "create an annotated bar to match the image (use height of the output image)",
-      "<fname.png>"],
-   
-   ['Image range and lookup table options', 'section' ],
-   ['-range', 'float',   2, \@{$opt{'range'}},
-      'valid range of values for MINC file',
-      '<real> <real>'],
-   ['-image_range', 'float', 2, \@{$opt{'image_range'}},
-      'range of image values to use for pixel intensity',
-      '<real> <real>'],
-   ['-auto_range', 'boolean', 0, \$opt{'auto_range'},
-      'automatically determine image range'],
-   ['-lookup', 'string', 1, \$opt{'lookup'},
-      'arguments to pass to minclookup',
-      '<\'argument list\'>'],
-   
-   ['Slicing options', 'section' ],
-   ['-transverse', 'arrayconst', ['zspace'], \@{$opt{'dirs'}},
-      'get a transverse slice'],
-   ['-axial', 'arrayconst', ['zspace'], \@{$opt{'dirs'}},
-      'synonym for transverse'],
-   ['-coronal', 'arrayconst', ['yspace'], \@{$opt{'dirs'}},
-      'get a coronal slice'],
-   ['-sagittal', 'arrayconst', ['xspace'], \@{$opt{'dirs'}},
-      'get a sagital slice'],
-   ['-allthree', 'arrayconst', ['zspace', 'xspace', 'yspace'], \@{$opt{'dirs'}},
-      'you probably dont want this, it is somewhat broken, use -triplanar instead'],
-   
-   ['triplanar options', 'section' ],
-   ['-triplanar', 'boolean', 0, \$opt{'triplanar'},
-      'create a triplanar view of the input MINC file'],
-   ['-tilesize', "integer", 1, \$opt{'tilesize'},
-      "pixel size for each image in a triplanar"],
-   ['-sagittal_offset', "integer", 1, \$opt{'sagittal_offset'},
-      "offset the sagittal slice from the centre",
-      "<# slices>"],
-   ['-sagittal_offset_perc', "integer", 1, \$opt{'sagittal_offset_perc'},
-      "offset the sagittal slice by a percentage from the centre",
-      "<% offset>"],
-   ['-vertical', 'const', 'vertical', \$opt{'orientation'},
-     'create a vertical triplanar view (Default)'],
-   ['-horizontal', 'const', 'horizontal', \$opt{'orientation'},
-     'create a horizontal triplanar view'],
-   );
+# handle -man, -help or missing args
+pod2usage(-verbose => 1) if $opt{'help'};
+pod2usage(-exitstatus => 0, -verbose => 2) if $opt{'man'};
+pod2usage(-verbose => 0) && exit if ($#ARGV != 1);
 
 # Check arguments
-&Getopt::Tabular::SetHelp ($Help, $Usage);
-&GetOptions (\@opt_table, \@ARGV) || exit 1;
-die $Usage if ($#ARGV < 0);
+#&Getopt::Tabular::SetHelp ($Help, $Usage);
+#&GetOptions (\@opt_table, \@ARGV) || exit 1;
+#die $Usage if ($#ARGV < 0);
 
 # create temporary directory
 $tmpdir = &tempdir( "$me-XXXXXXXX", TMPDIR => 1, CLEANUP => 1 );
@@ -520,3 +465,197 @@
       system(@_) == 0 or die "\n$me: Failed executing @_\n\n";
       }
    }
+
+# print version information
+sub print_version_info {
+   my $PACKAGE = '@PACKAGE_NAME@';
+   my $VERSION = '@PACKAGE_VERSION@';
+   my $PACKAGE_BUGREPORT = '@PACKAGE_BUGREPORT@';
+   
+   print STDOUT "\n$PACKAGE version $VERSION\n".
+                "Comments to $PACKAGE_BUGREPORT\n\n";
+   exit 0;
+   }
+
+__END__
+
+=head1 NAME
+
+B<mincpik> - generate images from minc files
+
+=head1 SYNOPSIS
+
+B<mincpik> [options] <infile>.mnc [<image.type>]
+
+mincpik generates image files from MINC volumes using the Imagemagick
+convert utility. Use -help or -man for more information and examples
+
+=head1 DESCRIPTION
+
+B<mincpik> generates image files from MINC volumes using the Imagemagick
+B<convert> utility. For a complete list of output file types see the
+B<convert> man pages.
+
+EXAMPLES:
+To display a default view, axial (z) slicing, middle slice
+using display. (display is part of the Imagemagick package)
+
+   mincpik infile.mnc PNG:- | display -
+
+To generate a PNG file of the 15th coronal slice
+
+   mincpik -slice 15 -coronal infile.mnc outfile.png
+
+To generate a JPG file using the hotmetal lookup table 
+with the image range 0 to 100
+
+   mincpik -lookup '-hotmetal' -image_range 0 100 infile.mnc outfile.jpg
+
+ImageMagick:  http://www.wizards.dupont.com/cristy/ImageMagick.html
+   NB: ImageMagick should be compiled without 16-bit quanta.
+
+Currently if there is a time dimension in the file the image will
+only produced from the first time point
+
+Problems or comments should be sent to: a.janke\@gmail.com
+ 
+=head1 OPTIONS
+
+=over 4
+
+=item B<-v>, B<--verbose>
+
+Be noisy when doing things
+
+=item B<--version>
+
+Print version number and exit
+
+=item B<-?>, B<--help>
+
+Dump some quick help output
+
+=item B<--man>
+
+Dump a man page
+
+=item B<-c> B<--clobber>
+
+overwrite the output file if it exists already
+
+=item B<-f> B<--fake>
+
+do a dry run, (echo cmds only). This is usually used in combination with -verbose to echo commands only
+
+=item B<--scale>
+
+scaling factor for resulting image, by default images are output 
+at twice their original resolution
+
+=item B<--width>
+
+autoscale the resulting image to have a fixed image width (in pixels)
+
+=item B<--depth>
+
+bitdepth for resulting image 8 or 16 (MSB machines only!)
+
+=item B<--title>
+
+add a title to the resulting image, if just this option is specified the text used for the title is the name of the input image file.
+
+=item B<--title_text>
+
+use the input string for the title [default: input-filename]. This option must be used in conjunction with -title
+
+=item B<--title_size>
+
+font point size for the title
+
+=item B<--anot_bar>
+
+create an annotated bar to match the image (use height of the output image)
+
+
+=head3 Image range and lookup table options
+   
+=item B<--range>
+
+valid range of values for MINC file
+
+=item B<--image_range>
+
+range of image values to use for pixel intensity
+
+=item B<--auto_range>
+
+automatically determine image range using a 5 and 95% PcT. (histogram)
+
+=item B<--lookup>
+
+arguments to pass to minclookup
+
+
+=head3 Slicing options
+   
+=item B<-s> B<--slice>
+
+slice number to get. (note this is in voxel co-ordinates)
+
+=item B<-z> B<--axial> B<--transverse>
+
+get an axial/transverse (z) slice
+
+=item B<-y> B<--coronal>
+
+get a coronal (y) slice
+
+=item B<-x> B<--sagittal>
+
+get a sagital (x) slice
+
+
+=head3 Triplanar options
+   
+=item B<-t> B<--triplanar>
+
+create a triplanar view of the input file
+
+=item B<--tilesize>
+
+pixel size for each image in a triplanar
+
+=item B<--sagittal_offset>
+
+offset the sagittal slice from the centre
+
+=item B<--sagittal_offset_perc>
+
+offset the sagittal slice by a percentage from the centre
+
+=item B<--vertical>
+
+create a vertical triplanar view (Default)
+
+=item B<--horizontal>
+
+create a horizontal triplanar view
+
+
+=back
+
+=head1 SEE ALSO
+
+convert(1) mincextract(1) display(1)
+
+=head1 AUTHOR
+
+Andrew Janke - a.janke@gmail.com
+
+=head1 COPYRIGHTS
+
+Copyright 2012 by Andrew L Janke
+
+=cuts
+
+