createdwiatlas:MainPage

From NITRC Wiki

1 INSTALLATION
- 1.1 From Source
- 1.2 As a Slicer extension
2 DOCUMENTATION
3 REFERENCES

INSTALLATION

From Source

 svn checkout https://www.nitrc.org/svn/createdwiatlas

1. Use cmake to generate the Makefile:

 createdwiatlas/ > ccmake .

and hit 'c'. It will ask for a local Slicer3 installation. Set SLICER_DIR to point to where your Slicer3-build is located, and hit 'c' again. Then hit 'g' to generate the Makefile. 'q' to quit.

2. Run make

At the terminal, type 'make':

 createdwiatlas/ > make

3. Test the binaries

Once the source has compiled, you can test the binaries by typing 'make test':

 createdwiatals/ > make test

This checks that each binary exists and that they successfully run with the flags '--help' and '--version'.

4. Test the modules

Each module has a test folder with one or more test scripts within. To test the modules, you can run these scripts. They also show how to run the modules from the commandline.

As a Slicer extension

(Once the modules are registered as Slicer extensions you will be able to download them directly from Slicer)

DOCUMENTATION

Each module corresponds to a step in creating a DWI Atlas:

1. Groupwise Registration: Co-register a set of subjects using their FA maps

2. Warp DWI's: Use the deformations computed by the registration to warp each subject's DWI

3. Average DWI's: Average the set of warped DWI's to produce the final DWI atlas

1. Groupwise Log Domain Symmetric Registration

IO: Images from which the atlas will be created These must be 3D images, for example, FA maps; Output Directory Where the intermediate and result images will be saved; Output Image suffix

Registration Parameters: Number of Outer Iterations The number of times the set of images are registered to a template; Levels The number of levels in the multi-resolution pyramid used to compute the registration from an image to the template; Number of Iterations per level The number of iterations used to compute the registration for each level of the multi-resolution pyramid; Starting smoothness of deformation Parameter that specifies amount of smoothing in the begining of the registration process; Final smoothness of deformation Parameter that specifies the amount of smoothing at the end of the registration process; Inversely proportional to gradient step size Parameter to specify the gradient step size

2. Warp DWI's

IO: Input Image A 3D image or 4D DWI image; Warp Image A 4D deformation image; Output Image; Resample at a) Canonical b) Original The gradient directions of the output image; Save the output image without the baseline slices? An option to save the output image without the B0 slices

3. Average DWI's