ImageK
Registration of T2 and Dess MR sequences
Ken Urish 2012


Important notes:
1. Questions with installation or operating?
Please email Ken Urish - ken.urish@gmail.com
Modifications to the software can easily be made if you are having trouble or processing images in bulk.
2. PLEASE READ THE ARTICLE - Registration of Magnetic Resonance Image Series for Knee Articular Cartilage Analysis – data from the Osteoarthritis Initiative
3. The code and software is offered under the BSD licence


To install the software - ImageK:
1. Unzip imageKinstall.zip
2. Select the imageK installer: Install_ImageK.exe
3. Follow the directions



To operate the software - ImageK
1. IMPORTANT: Place the images you want to register in the same directory as the ImageK.exe file.
This is soon going to be changed so that you can select the image files from anywhere.
2. If you want to only register one image, select "Register One File". Select the folder that contains the T2 sequence for the fixed folder and the DESS sequences for the moving folder. Hit OK.
3. If you want to register a large series of images (ie from the OAI), select the tab delineated text file that contains a list of the image names to register. Directions of notation to list filenames include: 
	a. <Path name of DESS folder>
	b. <tab> or <return> 
	c. <Path name of T2 map folder>
	d. <tab> or <return>

For example:
0.C.2\9093584\20041011\10128512
0.C.2\9093584\20041011\10128517
0.E.1\9117692\20050909\10499812
0.E.1\9117692\20050909\10499817

Will register the T2 and Dess images from the initial baseline time point from patients 9093584 and 9117692.
This text file can easily be created from the csv file provided by the OAI after an image request with editing in excel and saving as a tab delineated txt file. 
4. The remainder of the input settings can be tweaked after review of the itk registration engine in the itk software guide.

REMEMBER - that the Image folders must be in the folder that contains imageK.



The raw code:
1. The actual C++ itk files, the cmake file can be downloaded on the imageK website.
2. IMPORTANT: Use an itk version prior to 2009 - the registration engine changed its reference points after this time period and use of a later version would grossly alter accuracy. ITK v3.0 is currently in beta testing. Once the official ITK v3.0 is released the ImageK code will be updated to be compatable with this new version.