**fScan Reference Manual, Chapter 1 (Topics): Introduction**
===== Introduction -- Basic Introduction to fScan =====

[[jvs:fscan:overview|fScanOverview]]

[[jvs:fscan:manual:chapter1:differences|Differences between fScan and other fMRI packages]]

[[jvs:fscan:manual:chapter1:download|Downloading and installing]]

[[jvs:fscan:manual:chapter1:tutorial|Tutorial]]


====Overview Example====
Before attempting to analyze your own data you should look at a simple sample data set to get a feel for fScan's commands and interactive options.

[[jvs:fscan:manual:chapter1:tutorial|Sample Data Tutorial]]

====Organizing your data files====
Using fScan will generally involve Functional, Anatomical, and Behavioral data files. Any number of different types of files can be linked and processed together in a single data [[jvs:fscan:manual:chapter1:workspace_file?s[]=workspace|Workspace]]. A complete description of a data Workspace can be stored in an XML workspace descriptor file ([[jvs:fscan:manual:chapter1:workspace_file?s[]=workspace|WDF]]). When running fScan you can have it load your various data files separately, or they can all be loaded together simply by accessing the workspace WDF file.

[[jvs:fscan:manual:chapter1:functional_and_anatomical_images|Functional and Anatomical Images]]

[[jvs:fscan:manual:chapter1:behavioral_data|Behavioral Data]]

====Useful Tools====

[[jvs:fscan:manual:chapter1:visualization|Visualization]]

[[jvs:fscan:manual:chapter1:atlases|Atlases]]

[[jvs:fscan:manual:chapter1:thresholding|Thresholding]]


**See Also:**\\
[[jvs:fscan|fScan Home]], 
[[jvs:fscan:manual|fScan Manual]], 
[[jvs:fscan:manual:chapter1|Topics]], 
[[jvs:fscan:manual:help|Manual Help]]