Install OSX processing tools

Outline

Mac OS X Tools - Info

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This document was written to help you find and install most of the tools we use here at the Brainmapping Center (on Mac OS X 10.2 ONLY). Please read carefully, follow the instructions and you will be up and running in no time (well, there is the download time...)

1. What tools are we talking about?
2. Where do I find the tools?
3. OK, but which tools do I need and how do I install them?

What tools are we taking about?

Here at the Brainmapping Center we use the following tools (listed in no specific order):

• FSL - "a comprehensive library of functional and structural brain image analysis tools."
• AFNI - "a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data."
• UCLA Tools - a set of various tools (command line only) created by Mark Cohen here at the Brainmapping Center.
• AIR - a set of tools that are used for "automated registration of 3D (and 2D) images within and across subjects and within and sometimes across imaging modalities."
• xds - a very popular and widely used display tool for MGH-style format image data.
• MATLAB and SPM - no, we are not going to distribute MATLAB or SPM here, but we are going to tell you how to make it work on OS 10.2.
• X11 - a free (at least for now) implementation of the X Window System for Mac OS X created by Apple and based on Xfree86. This is needed to run FSL, AFNI, MATLAB and xds.

We also provide samples of resource files:

• Resource Files - Folder'RC_Files' at www.brainmapping.org contains examples of resource files some of which you will need and some that are just nice to have (they can make life a little bit easier). NOTE: these files should be saved in your home directory, and they should have a . (dot) in front of the name, but we could not load them like that here (they would not show on out ftp site). Instead these files are loaded as simple text files, and when you click on them they will display in the browser. You can view them and then modify your existing resource files, or you can download them (or you can just cut-and-paste from your browser directly to a text editor of your choice - make sure that you save as plain text). If you download them, first rename them from 'something' to '.something', and then save them in your home directory.
  1. tcshrc (.tcshrc) or cshrc (.cshrc) - these are important and you should have one in your home directory (you don't need both; in fact, if you do, only one will be read and executed (I believe .tcshrc takes precedence) that sets a correct path to all of the tools and also uses an alias file for the shortcuts. You can easily set up you .tcshrc (or .cshrc) file with the same paths because the tools you have installed are in the same directories as in this example file. You can also find an example of .cshrc (could easily be called .tcshrc) file here, which does not set paths. By setting paths as in the first example, you will be able to start any of your tools from the command line. If you try to start afni (for example) and type 'afni', but the system tells you 'command not found' your problem is probably in incorrect path. If you do not set your path this way, you can still start your tools, but you need to specify the whole path to the executable( e.g. type /usr/local/bin/afni/afni to launch afni).
  2. xinitrc (.xinitrc) NOT USED WITH X11- this is an initialization file for X Windows and this one in particular is used if you are using mwm as your window manager. The commands in this file will be executed when your XWindows are starting (this one will start mwm and open three windows). There are many more commands that you can put here, but this is the minimum.
  3. afnirc (.afnirc) - some environment variables. Not needed, but will not hurt.
  4. gnuplot (.gnuplot) - some variables for gnuplot. Again, not necessary, but nice to have.
  5. alias (.alias) - some example shortcuts. Note that this file is called from .tcshrc or .cshrc. This is useful if you are using some commands repeatedly - saves time on typing. You don't need this file, but it helps.

Where do I find the tools?

You can find links to all the tools on the Installation Instructions page.

OK, but which tools do I need and how do I install them?

For this too, see Installation Instructions.