Diffeomorphic Multimodal Image Registration using RaPTOR
This code is based on Fourier-Approximated Lie Algebras (FLASH). FLASH can be downloaded from https://bitbucket.org/FlashC/flashc/src/master/
The instructions to install DiffeoRaptor is similar to the one in the above link. You can find the same steps below:
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Step 1: Install Armadillo
The version of Armadillo >= 3.920 http://arma.sourceforge.net/download.html
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Step 2: Install Pyca Pyca can be downloaded from https://bitbucket.org/scicompanat/pyca. Follow the steps closely. Pay attention to software requirements and their version. You need specific version of your c++ compiler and other tools to successfully install Pyca. You can switch off the GPU functionality in Pyca since this is not required in our code.
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Step 2: After unzipping the DiffeoRaptor.zip, in your terminal:
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cd DiffeoRaptor
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ccmake .
Specify Pyca source code, and Pyca binary path
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make
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The DiffeoRaptor software package contains several functions for image processing as well as example script files to run the software.
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In the folder DiffeoRaptor/Testing/runO3test you can find two example scripts. For running DiffeoRaptor, use "diffeoraptorO3_IXI.sh". For evaluating the Dice score use "processResults.sh". You need to modify both scripts based on your current directories and preffered parameter settings.
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The scripts run the cxx files in the parent directory (DiffeoRaptor/Testing). In order, to modify the functionality, you will need to modify those cxx files.
Please cite our IJCARS paper and the FLASH paper in case you used the code in your project:
[1] N. Masoumi, H. Rivaz, M.O. Ahmad, and Y. Xiao, DiffeoRaptor: diffeomorphic inter-modal image registration using RaPTOR. Int J CARS (2022). https://doi.org/10.1007/s11548-022-02749-2
[2] M. Zhang and P. T. Fletcher, “Fast Diffeomorphic Image Registration via Fourier-Approximated Lie Algebras”, In International Journal of Computer Vision 2019, 127, 61–73. https://doi.org/10.1007/s11263-018-1099-x
[3] M. Zhang and P. T. Fletcher, “Finite-Dimensional Lie Algebras for Fast Diffeomorphic Image Registration”, In Information Processing in Medical Imaging. IPMI, 2015. Lecture Notes in Computer Science, vol 9123. Springer, Cham. https://doi.org/10.1007/978-3-319-19992-4_19
In case you have a question, don't hesitate to post in "Issuses" or contact the first author by: n_masoum@encs.concordia.ca