Imaging resources

Preparing for fMRI data analysis within SPM

This is a basic overview for preparing to run functional MRI analysis.

1. Install Matlab.

You can install Matlab direct from the Mathworks site, and can start with a free trial if needed.  At Yale your lab or department may have a license that allows you to download and use this for free.  If you are purchasing software through your department you can order Matlab at a discount from Yale's software archive.

2. Install SPM.

There are detailed instructions with the SPM software and add it to your path so that you it runs without issue.

3. Install the artifact detection toolbox (ART).

The ART toolbox by Sue Gabrielli and colleagues is particularly useful in imaging analysis.


The following are optional but recommended –

4. Install xjView viewing software.

xjView is a particularly useful toolbox for viewing imaging data at different thresholds within SPM.

5. Installing FSL, Oxford's image analysis package, is also very useful if you are happy to spend up to 5GB to do so.  Apart from FSL being perhaps a nicer software package in many ways, if you are using SPM FSL has a large number of intuitive, easy-to-use command-line tools to manipulate images and a particularly nice image viewer.  The latter is actually particularly helpful in artifact detection, and preparing images for publication.

6. Install itk-Snap.  There are many tools for drawing Regions of Interest.  ITK-snap is effective and easy to use.