AIR Pipeline Workflow Plugin

User Manual

Introduction

The Automated Image Registration (AIR)-based plugin allows the user to create template and register pre- and post- injection mouse brain images in Analyze Image format using the command-line execution of LONI Pipeline workflows (LONI Pipeline).

Getting Started

To use the AIR-based image template creation and registration plugin:

1. Open the Registration Workspace.
2. Add and select the Source and Template data
3. Select the AIR Pipeline Workflow item in the Registration Method combobox. If successful, Pipeline Methods drop-down menu will be displayed in the workspace, along with the I/O-paths window and the command-line output window.

File Formats supported

1. Analyze Image (16-bit)

Cart objects supported

1. derived class of Image3D

User interface

• Choosing pipeline method:
  1. Select method from drop down menu.

Functional Specification

1. 1. Create Template method aligns Source images to template image and creates a template based on aligned source images which is saved to the location specified in "Output filename path".
   2. Register Pre-injection method registers source images to the template image. The output of this step are the source images that are in the same space as the template image. The transformation matrices are also saved to be used to register post-injection images.
   3. Register Post-injection method applies the transformation matrices saved from Register Pre-injection step to the appropriate source images to put them in the same space.

Workspace Interoperability

Error Handling

DarenLee^? - 04 May 2009