Using Cmgui Digitiser

When using digitizer – visiblehuman.com (you can find the script from the following site: http://cmiss.bioeng.auckland.ac.nz/development/examples/a/visiblehuman/index.html) Please be aware of using “{” and “}”brackets at the beginning and end of the script, for example:

The changes I have made to the script (which allow me to have a enormous amount of group names) requires adding of “{” and “}”at the beginning and end of the script. By doing this, the program will execute command such as “my $ NAME = … “ (the original script without “{” and “}”at the beginning and end would not do this!). So if the original script has the command such as “my $glyphSize = 20”, you’d better comment it out. Otherwise the programme will use $glyphSize = 20 instead of $glyphSize = 1, and when you are doing your digitising the giant glyph points will appear!

(I sincerely hope you understand what I am talking about – because my friend doesn’t, also I will attach the changes of the code I made. The command lines with # mark were the original scripts)

{

# Without the curly bracket "{" and "}" at the beginning and end of the script respectively, the command won't execute "my $name" # So this script uses the default glyphType of sphere and size of 1.

use CmUtils::Digitise qw( cmguiInit checkImageSet setDataGroups loadExdataGroup digitiseSlices splitExdata setGlyphs); use CmUtils::Digitise::Echo qw( Echo_CreateImageSet );

# Variables user should change #-----------------------------

# Default glyph values: #my $glyphType = "sphere"; #my $glyphSize = 20;

$datafile = "traces";

#%groups = qw(marker gold lvendo red rvendo green epi blue stomach bone skin purple skinlleg tissue skinrleg red spinalCord white liver bluey)

my %groups; $groups{'neck'} = 'red'; $groups{'marker'} = 'gold'; $groups{'lvendo'} = 'red'; $groups{'epi'} = 'blue'; $groups{'rvendo'} = 'green'; $groups{'stomach'} = 'bone'; $groups{'skin'} = 'white'; $groups{'skinlleg'} = 'tissue'; $groups{'skinrleg'} = 'red'; $groups{'spinalCord'} = 'white'; $groups{'liver'} = 'purple'; $groups{'esophagusinner'} = 'red'; $groups{'esophagus'} = 'green'; $groups{'duodenum'} = 'gold'; $groups{'largeIntestine'} = 'green'; $groups{'smallIntestine'} = 'bluey';