wiki

Imaging

Software and Tools

• SPM Statistical Parametric Mapping for different types of neuro data
• FSL A unix based tool for neuroimaging analysis
• AFNI I’ve only used it for the AlphaSim tool
• conn A toolbox for resting connectivity analysis based in MATLAB
• xjView A simple tool for displaying images and overlays
• xvfb Allows sending graphical output to spot in memory, useful for graphical functionality in cluster environment
• Rdgehdr Used to convert pfiles into text to read header info!
• MRICron a nice tool to have for looking quickly at data, and figuring out orientation. It comes with a package called - dcm2nii that converts DICOM–>NIFTII as well.

Data Preparation

• Quality Checking Tools
• Neuroimaging Orientation
• Voxel Value Matrix Using a combination of scripts in Matlab, SPM, and bash to produce a matrix of raw activation values for each voxel from a functional set.
• Running Scripts Contains general information about running bash and python scripts on the cluster.