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MIPAV Documentation for the end-user

There are three documents on how to use MIPAV:

  • User Guide: the complete end-user information on MIPAV, including installation, use and technical conformance;
  • Frequently Asked Questions (FAQ): answers to commonly asked questions;
  • How-To: a quick guide with step-by-step instruction on complex tasks;
  • Presentations: a collection of presentation slides that the MIPAV group has used in classes and displays.

You will need free Adobe PDF Reader to view the following files.

User Guide

Volume 1: Basics

You may download the entire Volume 1 as a single PDF.



  1. Introducing MIPAV
  2. Installing MIPAV
  3. Getting Started Quickly with MIPAV
  4. Understanding Image Basics
  5. Working with DICOM Images
  6. Connecting to SRB BIRN
  7. Visualizing Images
  8. Segmenting Images Using Contours and Masks
  9. Analyzing Images
  10. Changing Image Datasets Using MIPAV Utilities
  11. Using Scripts (Macros) in MIPAV
  12. Developing Plugin Programs



  1. References
  2. DICOM Conformance
  3. Technical Information

Volume 2: Algorithms

Volume 2 details the algorithms that are available for use in MIPAV.

For the time being, Volume 2 of the userguide is collected as a single PDF.

How To

MIPAV technical instruction guides

The MIPAV group presents technical instruction guides to assist users perform operations with MIPAV that have a complex number of steps, but that are scientifically significant or will present interesting results. Techinical instruction guides answer the question of how-to accomplish a task in MIPAV. However because of the complex nature of these instructions, they are not suitable for the general nature of the user-guide; instead we present these guides here.

We expect there will be a number of interesting guides, but these guides take a while to generate with complete instructions.

Using MIPAV to Label and Measure Brain Components in Talairach Space
Using the Insight Toolkit (ITK) from within MIPAV
Using Fluorescent Resonance Energy Transfer (FRET) algorithms in MIPAV

Other interesting technical guides will be forthcoming.


MIPAV group gives classes on using MIPAV and prepares presentations. Presented here are the slides used in those presentations. Not all presentations here are from classes; some slideshow presentations are taken from speeches and talks made by group members or collaborators which describe how to perform certain functions within MIPAV or how to interperet certain kinds of results.

MIPAV classes

From classes within the CIT training program.

Getting Started with MIPAV
MIPAV Algorithms
Plugin Development
Segmentation and Annotation
Visualization Using MIPAV

General Presentations

From presentations outside the MIPAV classes


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