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ISIS wiki

Welcome to ISIS, the medical data integration toolkit. The ISIS project aims to provide a framework to access a large variety of image processing libraries written in different programming languages and environments. Its special purpose is to handle multidimensional image data from the field of neuroimaging or similar medical applications. This first implementation will provide an interface to the Insight Toolkit (ITK) and the Lipsia fMRI-Data Analysis Toolkit.

Documentation

To get you started, there are a number of documents:

Remember!: The Developer documentation should provide an in-depth discussion of the API and how to use it in complex situations The TUTORIALS section in contrast should contain small articles, describing how to get things working, quick and dirty. Optional, they can provide links to related in-depth articles from the developer docu.

Introduction

• Installation on various platforms
• basic tools usage
  • isisconv
  • isisdump
  • isiscalc
  • isistransform
  • isisview
• HowTo build the source code
  • Linux
  • Windows
  • Mac
• programming tutorials C++
  • the basics
    • a minimal isis application
    • basic math on voxel data (naive version)
    • basic math on voxel data (iterator version)
    • logging to a file
• real world application examples
  • extract diffusion directions and write the corresponding 4D data
  • doing per voxel math
  • averaging voxels based on a mask and a threshold
  • removing volumes from timeseries
  • find sagittal images with python
  • cut slices at top/bottom

Developers

• The doxygen generated API documentation can be found at http://isis-group.github.com/isis/doxygen/index.html

• Core

  • the dynamic type system
    • convert via lexical mapping
    • automatic conversion of value objects
  • property mapping
  • the chunk concept
  • image data
  • the logging system
  • error handling
  • common metadata

• ImageIO plugins

  • Plugin API
  • Property constraints
  • Examples

• Extension plugins

  • Extension API
  • Property constraints
  • Examples

• Python API

• testing rules and tools

File Formats

• vista
• nifti
• dicom
• bruker

ImageIO Plugins