After struggling a long time with installing it, the developer pointed me in the right direction (thank you!), a blog helped me too (thanks!) which led me to installing it correctly. If it may help you, this is exactly what I did:

1. Install MIPAV 7.0.2 via http://mipav.cit.nih.gov/download.php

Standard install to /Applications – choose different folder if there are issues with admin rights

2. Install CBS Tools 3.0.4 via https://www.nitrc.org/frs/?group_id=606

Choose CBSTools-release-3.0.4-150106.jar, external-scripts.jar and jist-cruise-3.0.1.-140716.jar

Start MIPAV, click Plugins > Install plugin; navigate to folder with *.jar files, select them, click >, click ‘Install Plugins’

Copy *.jar files to Mipav plugin folder, usually ~/mipav/plugin

3. Open MIPAV, click Plugins > jist* > JISTLayoutTool

Click Project > Global Preferences

Select same directories as in step 4, click save, close JIST, close MIPAV.

4. Open file mipav/plugin/directory/run-cbstools-mac and modify:

JAVALIB=/mipav/installation/directory/jre/Contents/Home/lib/ext/

MIPAV=/mipav/installation/directory

PLUGINS=/mipav/plugin/directory

5. In terminal, cd to /mipav/plugin/directory

To make sure there are no carriage return line feeds:

tr -d ‘\r’ < run-cbstools-mac > run-cbstools-mac2

(You can modify name at the end, to your liking)

To make it executable:

Chmod +x run-cbs-tool-mac2

Run with command in terminal ‘run-cbstools-mac2’

If you would like to run it anywhere, make sure to add /mipav/plugin/directory to your .bash_profile (export PATH=$PATH:/mipav/plugin/dir) and possibly a shortcut (eg alias cbstools=’/mipav/plugin/directory/run-cbstools-mac2′).