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1.
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Answer
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for
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MAX
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Installation
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Questions.
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The
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best
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way
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to
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know
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if
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the
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installation
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is
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correct
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is
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to
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enter
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the
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following
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command:
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./max.pl
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--help
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If
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it
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shows
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the
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in-line
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help
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text
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(over
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800
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lines
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of
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text),
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the
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installation
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is
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correct.
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If
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some
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of
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the
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Perl
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modules
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are
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missing,
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you
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will
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see
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errors
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that
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look
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like...
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Can't
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locate
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Math/Polygon/Calc.pm
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in
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@INC
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(@INC
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contains:
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/usr/lib/perl5/...
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/usr/lib/perl5/5.8.0
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/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
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BEGIN failed--compilation
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aborted
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at
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...
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MAX
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is
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written
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in
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Perl.
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2.
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Additional
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Perl
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Modules
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Needed
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for
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MAX.
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It
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looks
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like
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there
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are
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some
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Perl
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modules
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that
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need
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to
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be
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installed.
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And,
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yes,
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you
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can
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get
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them
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from
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CPAN
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(cpan.org):
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XML::Twig
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Tie::IxHash
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Math::Polygon::Calc
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(These
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are
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referenced
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by
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the
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"use"
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statements
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in
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the
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Perl
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code.)
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After
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installing
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these
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3
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modules,
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you
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should
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be
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able
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to
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get
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the
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correct
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output
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when
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you
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type
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"./max.pl
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-
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help".
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>I
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downloaded
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XML-Twig-3.32.tar.gz,
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I'm
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using
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version
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3.16,
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but
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I
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don't
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think
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this
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will
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be
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a
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problem.
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Twig
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might
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have
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some
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dependencies;
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if
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so,
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you'll
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have
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to
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install
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some
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other
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modules.
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For
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example,
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if
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you
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see
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an
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error
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message
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that
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says
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that
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it
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couldn't
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find
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XML/Xpath.pm,
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that
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means
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that
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you
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would
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need
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to
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download
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and
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install
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XML::Xpath
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also.
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>Tie-IxHash-1.21.tar.gz
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and
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Math-Polygon-1.00.tar.gz.
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These are the same version that I'm
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using.
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3.
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Install
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Additional
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Perl
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Modules
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in
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User
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Specified
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Directory
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Instead
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of
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the
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System
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Directory
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You
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can
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actually
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install
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the
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Perl
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modules
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anywhere
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-
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-
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for
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example,
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in
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your
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home
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directory,
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but
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maybe
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even
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better
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is
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to
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install
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them
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in
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MAX's
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directory.
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This
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article...
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http://tnerd.com/2008/10/26/perl-how-to-install-perl-modules-in-few-quick-steps/
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looks like it has a pretty good procedure for doing this using CPAN, but it does look a little complicated. I've never done it quite this way; instead, I just install modules manually. If you want to do it manually, read the section of this article under "Manual installation of the module as a normal user under home directory". Before doing this, you should decide on a directory that will hold all the Perl modules. Then read this section: "set the environment variable PERL5LIB pointing to the home directory" to tell Perl where the new modules will be located.
4. Using MAX
MAX will analyze the XML files and will perform nodule matching. I believe that the XML files that you get from us are in the form of a single file that contains the unblinded reads from 4 LIDC sites merged into one file. If so, here's an example of how you would run MAX to do the matching: max.pl --fname mergedfile.xml --skip-num-files-check
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--pixel-size=0.7
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--slice-spacing=1.0
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--xml-ops=
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none or since MAX lets you abbreviate most of the command line options, this also works... max.pl --fname mergedfile.xml --skip --pixel=0.7
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--slice=1.0
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--xml-ops=
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none A couple of comments:
* You might need to include a path on MAX depending on how and where it was installed.
* You might need to include a path to the merged file. But you will probably run MAX from the directory that contains the file.
* Instead of the values shown above, you will have to get the *true* pixel and slice spacing for the series that corresponds to the merged file. **MAX will not work properly unless you have the correct values for both** You can get the values from looking at the DICOM files. Note that you'll have to look at two adjacent files to get the slice spacing; there is no single DICOM tag that gives this value.
* Just for testing, I recommended that you run MAX with "--xml-ops=none"
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as
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shown
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above
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which
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prevents
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any
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XML
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files
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from
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being
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written.
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We
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can
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talk
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about
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this
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later.
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So
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for
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now,
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all
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the
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results
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(along
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with
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A
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LOT
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of
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other
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info)
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will
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be
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printed
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to
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the
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screen.
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5. slice-spacing
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Error
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(6501)
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results
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if
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the
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slice
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spacing
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is
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wrong.
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Here's
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one
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way
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to
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get
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the
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slice
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spacing
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from
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the
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DICOM
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images:
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The
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most
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reliable
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DICOM
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tag
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to
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use
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is
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"Image
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Position
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Patient"
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(0020,0032).
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A
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typical
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dump
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of
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this
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tag
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from
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an
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image
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looks
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like
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this:
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0020 0032 34 // REL Image Position
Patient//-209.800003-193.600006-72.199997
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It
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is
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a
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Type
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1
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tag,
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so
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it's
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always
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going
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to
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be
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present
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and
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should
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be
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reliable.
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Since
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CT
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images
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are
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axials,
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the
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z
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position
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of
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each
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image
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is
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the
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final
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coordinate
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number:
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-72.2mm
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in
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this
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case.
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The
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most
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reliable
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way
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of
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doing
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this
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is
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to
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extract
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the
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z
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coordinates
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from
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all
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the
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images,
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sort
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them,
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and
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then
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see
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what
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the
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delta-z
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value
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is.
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(Watch
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out
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when
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parsing
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these
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lines:
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The
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"\"
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can
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cause
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problems
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if
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the
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numeral
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immediately
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following
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it
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is
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a
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0
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(zero).
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In
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many
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programming/scripting
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situations,
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"\0"
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represents
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a
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null
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which
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could
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signal
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the
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end
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of
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the
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string
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!
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!)
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6.
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pixel-size
Here's a dump from a DICOM file:
0028 0030 30 // IMG Pixel Spacing//007.421880e-01\007.421880e-01 Once
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again,
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watch
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out
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for
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the
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"\"
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!
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!
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Note
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that
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this
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tag
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gives
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the
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spacing
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in
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both
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in-plane
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directions,
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but
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our
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pixels
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always
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seem
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to
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be
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square,
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so
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we
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don't
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need
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both
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numbers.
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