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ROIbuilder

ROIbuilder is a quick little Python script that allows one to specify a set of Regions Of Interest from the Talairach and Brodmann atlases, and create an AFNI mask covering those regions. The whereami tool in the AFNI suite performs a similar function for a single region. ROIbuilder is a wrapper around whereami and 3dcalc that lets you easily put together many such masks.

Download and Installation

ROIbuilder is a Python script built using Glade, and so you will need the GTK tools and PyGTK. Many distributions already have these tools, as they are a nice way to quickly build such things as this.

Download ROIbuilder.tgz. Version 20080119.

Unpack into any convenient directory, and create a symbolic link to the main script in your bin:

tar -xzvf ROIbuilder.tgz
cd ROIbuilder
ln -s `pwd`/ROIbuilder ~/bin

Usage

Run ROIbuilder. Name the mask using the Mask Brik Prefix box, and select regions (using shift+click and control+click). For example, to create a mask of the cerebellum:

Then, push the Generate mask button, and the mask is created. Here's what it looks like in AFNI:

By default, the mask will be created on a 1x1x1 mm grid. If you enter an AFNI dataset name in the Mask Template box, that dataset will be used to define the grid for the mask. Such masks are useful with 3dROIstats, for example.