Spamalize Installation Manual

This webpage is the primary source for installation instructions for Spamalize for both the compiled (VM) version and for the full (source-code) version.

Table of Contents:

  1. Introduction
    1. Encouragement
    2. Conditions for Use
    3. Disclaimer
  2. Installation Instructions
    1. Download
    2. IDL Virtual Machine (FREE!) installation
    3. Full installation (with Spamalize source code)
  3. Programming Hints

      I. Introduction:

      Spamalize is an interactive software package for analysis and display of medically-related research data. Spamalize was originally designed to analyze PET and MRI data, but has evolved into a GUI-driven environment versatile enough for many imaging formats.

      Spamalize requires the IDL environment. This is a commercial software environment available from RSI, and a free RunTime version is now available. Spamalize can run on unix (SUN, etc.), linux, Windows, and MacIntosh (OS-10 or better). The same files are used on all of these different operating systems, so you only need to download and install a single set of Spamalize files.

      A. Encouragement and Disclaimer

      If you use Spamalize and find it helpful, please let the author know! Spamalize can be used free of charge by academic users. However, bearing in mind that there is no such thing as a free lunch, please consider including the author of Spamalize on the first published paper, abstract, etc. which uses Spamalize to perform a significant portion of the data analysis.

      A good criteria is that if you would have found it difficult or tedious to write the program that performed an important part of your analysis, you should share the credit- it was probably difficult and/or tedious to write the program the first time around... (You would not believe the number of people that forget about this requirement as they rush a paper off to press!) If you forget to include me as a coauthor, other gestures of gratitude are appropriate, such as buying me a beer at the next conference we attend.

      Conditions for Use: You are welcome to use Spamalize, subject to the following conditions:

      1. I ask that you do not distribute Spamalize to others. Instead, please direct inquiries to me, as I like to keep track of who is using it. Please include a brief description of your institution and your application(s) for Spamalize.
      2. If you use the code or any part of it in a commercial enterprise, you must first obtain my permission, and be prepared to pay a license fee.
      3. You should offer to include me on the first publication where Spamalize contributed in a significant way to your analysis, understanding or display of results.

      DISCLAIMER: I enjoy hearing feedback, and would be happy to modify Spamalize routines for individuals with interesting applications. However, expect no support unless you have made arrangements with me. You may use Spamalize only if you (or a representative of your organization) have received permission from the author, Terry Oakes. The author takes no responsibility for the results. It is the responsibility of each user to check the code, the input data, and the results for appropriateness.

      II. Installation Instructions:

      A. Download:

      Send an email to Terry Oakes (troakes - at - to receive download instructions. Please include your name, institution, and a brief (1-2 sentence) description of your project. The instructions will direct you to the ftp website where you can download the file(s).

      B. IDL Virtual Machine (free) Installation of Spamalize:

      The primary release of Spamalize is in the format of precompiled code designed to be run with the free "Virtual Machine" version of IDL. You first need to download and install the IDL Virtual Machine from RSI.

      At the Spamalize download site, click on the file "spam_VM.tar.gz" to download it. I suggest making a new directory:


      and putting it there, in a subdirectory of where IDL is installed. Then unzip and untar the file:

      - gunzip spam_VM.tar.gz

      - tar -xvf spam_VM.tar

      (Depending on your computer's settings, these last two steps may happen automatically.)

      Under IDL 6.1 and later, the current working directory is where the file "spam_VM.sav" is located that you invoke from the VM. Thus, the .sav file must be in the same directory as the "spamalize_defaults.txt" file, and the “data/” and “help/”directories must be subdirectories of the current working directory. Make sure this is so after you finish un-tarring the files. Also make sure the file "spamalize_defaults.txt" is in this directory. Finally, create a temporary directory at this level, called “temp”.

      After this, you only need to edit a single file to use Spamalize. Using a text-editor, open the file


      and follow the instructions there.


      The "tar" file was made with the help files sourced from ./src/help/, so (depending on how your tar-file gets extracted) you may need to move the help directory up one level so the help directory is in the same directory as the VM file "spamalize_rt_vm.sav". To call this program, under unix/linux or similar, type:

      idl_6.1 -vm='/apps/dev/spamalize/spamalize_rt_vm.sav'

      Under Windows/Mac, drag the file icon onto the IDL/VM icon.

      Limitations of VM relevant to Spamalize:

      1) Can't use EXECUTE procedure:

      Several (~20) Spamalize programs use the EXECUTE procedure, mostly to reinterpret strings containing variable information. This is not allowed in IDL-VM, since this would provide a sneaky backdoor to let VM users have "full" IDL. The programs or subroutines that use EXECUTE will crash when you try to use them. Most of the instances of EXECUTE in Spamalize are in fairly minor programs or little-used situations. Please let me know if your favorite program doesn't work under the VM version- we can probably fix it.

      2) No printout of information and error messages:

      In order to run Spamalize and get the output of what it creates you must run it from the commandline. Since the default action using VM is to simply start the Spamalize GUI, there is no place for the informational text messages to go. (In the normal, "full" version of IDL, these messages go to the IDL GUI or to the terminal window where you called idl from.) To get around this, you should try to call IDL-VM from a terminal window.

      Macintosh Installation: The following hints explain how Drew Fox installed Spamalize-VM on his brand spankin' new Macintosh laptop:

      Assuming a standard install, you must run:

      /Applications/rsi/idl/bin/idl -vm=/Applications/rsi/idl/spam_VM/spamalize_rt_vm.sav

      from inside a terminal window. Make sure you have X11 on your machines, and that the DISPLAY environment variable is set correctly. I think that RSI has instructions on how to do this, but it only really involves downloading the package from Apple, and not attempting to mess with your display (took me a few tries... since I messed with my display).

      I also simplified my task by putting the spam_VM directory in /usr/local, creating symbolic links to .../idl/bin/* in my /usr/local/bin directory (because it is always in my path). An alias called 'spam' to the above command should work, i.e. editi your .bashrc to include:

      alias spam='/Applications/rsi/idl/bin/idl -vm=/Applications/rsi/idl/spam_VM/spamalize_rt_vm.sav'


      Please read the "Conditions for Use". After that, you can get to work!


      C. Installation Instructions (IDL Full license):

      The source code for Spamalize is also available if you would like to poke around in the individual programs. To use it, you will need a full license for IDL from RSI. When you email Terry, let him know you want the source code.

      Download (e.g. ftp) a tar-ball file of SPAMALIZE onto your local disk system, maintaining the directory structure. Un-tar the files. The top-level SPAMALIZE directory is called (not coincidentally) "spamalize". Recommended (standard) locations for the spamalize directory are:

      unix/linux: /apps/
      Windows: C:\RSI\

      The disk where you put the spamalize temporary directory should be large enough to contain any image files that might get written there, and should have its write-permissions set so that anybody who uses SPAMALIZE can write to it. Otherwise, a crash will most likely result. Make sure that the directory


      is in the IDL path. In the IDLDE GUI, select "File->Preferences...", then select the "Path" tab, and "Add" the /.../spamalize/ directory to the path. Check the box to the left of the directory to include all subdirectories. After this, you only need to edit a single file to install Spamalize. Using a text-editor, open the file


      and follow the instructions there.

      And that's it! You are done with the installation. If you want to customize Spamalize or enhance its performance, here are some tips for power users and programmers.


      Please read the "Conditions for Use". After that, you can get to work!


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