Getting the tools

Checking out a copy from CVS

1. Add the following environment variables to your ~/.cshrc if you're using the t shell (username is your BIC username)

   setenv CVSROOT username@cvs.bic.mni.mcgill.ca:/private-cvsroot
   setenv CVS_RSH ssh

   or to your ~/.bashrc if you're using the bash shell (username is your BIC username)

   export CVSROOT=username@cvs.bic.mni.mcgill.ca:/private-cvsroot
   export CVS_RSH=ssh

2. Make sure you are in the directory where you want to install the package

   cd wherever

3. Get the latest release from CVS (check here to see the newest available releases, with known bugs and new features)

   cvs checkout -r Release-3 mincdiffusion

Building the source files on a BIC machine

1. Go into the mincdiffusion directory

   cd mincdiffusion

2. Use the build.sh script to setup paths for the build, note that you can now compile against minc2 libraries

   Usage ./build.sh VTK_DIR MINC_BASE_DIR [INSTALL_DIR]

   example: ./build.sh /usr/lib/vtk-5.0/ /usr/local/bic/ ./ (minc2)

   or example: ./build.sh /usr/lib/vtk-5.0/ /usr/local/mni/ ./ (minc1)

3. Build executables

   make

4. Install

   make install

5. All the necessary libraries should be available on local BIC machines, but you will need to install NIAK.
6. Make sure the bin directory (wherever/mincdiffusion/bin) is on your path, which is specified in your ~/.cshrc or ~/.bashrc (help here). Also add (wherever/mincdiffusion/bin) and wherever you installed NIAK (wherever/niak.x.x.x) to your matlab path (help here).
   NOTE: You MUST create a symbolic link from your bin to the matlab you want to call, an alias does not seem to work!
   

Building the source files on an external Linux machine

Tips for installing on Ubuntu Ubuntu install

Updating your version of the tools