1. Answer for MAX Installation Questions.<!-- /* Font Definitions */ @font-face
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-->The best way to know if the installation is correct is to enter the following command:
./max.pl --help
If it shows the in-line help text (over 800 lines of text), the installation is correct. If some of the Perl modules are missing, you will see errors that look like...
Can't locate Math/Polygon/Calc.pm in @INC (@INC contains: /usr/lib/perl5/...
/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi ...
BEGIN failed--compilation aborted at ...
MAX is written in Perl.
2. Additional Perl Modules Needed for MAX.
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-->It looks like there are some Perl modules that need to be installed. And, yes, you can get them from CPAN (cpan.org):
XML::Twig
Tie::IxHash
Math::Polygon::Calc
(These are referenced by the "use" statements in the Perl code.) After installing these 3 modules, you should be able to get the correct output when you type "./max.pl -help". <!- /* Font Definitions */ @font-face
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-->>I downloaded XML-Twig-3.32.tar.gz, I'm using version 3.16, but I don't think this will be a problem.
Twig might have some dependencies; if so, you'll have to install some other modules. For example, if you see an error message that says that it couldn't find XML/Xpath.pm, that means that you would need to download and install XML::Xpath also. >Tie-IxHash-1.21.tar.gz and Math-Polygon-1.00.tar.gz. These are the same version that I'm using.
3. Install Additional Perl Modules in User Specified Directory Instead of the System Directory <!-- /* Font Definitions */ @font-face
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-->You can actually install the Perl modules anywhere -- for example, in your home directory, but maybe even better is to install them in MAX's directory. This article... http://tnerd.com/2008/10/26/perl-how-to-install-perl-modules-in-few-quick-steps/
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
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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
--pixel-size=0.7 --slice-spacing=1.0 --xml-ops=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 --slice=1.0 --xml-ops=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" as shown above which prevents any XML files from being written. We can talk about this later. So for now, all the results (along with A LOT of other info) will be printed to the screen.