
Please use this identifier to cite or link to this publication: http://hdl.handle.net/10380/3469 |







This work describes a library for fitting kinetic models to dynamic PET and MR images.
Hypothesis:It is assumed that images of medical time activity curves can be read and standard kinetic models can be efficiently fit to the time activity curves given a blood input function.
Evidence:The authors present a library, "itk::ka" that contains classes to model time activity curves, blood input functions, and data in the for of 3D medical images. Also, there non-linear optimizers like the Powell-Dogleg optimizer and their corresponding cost functions. A number of models are also presented: AnalyticStd{2c,2ic,1c}, ExpSum{5k,3k}, and SimulatorOdeStd{1c,2ic,2c}. Driver executables and methods to specify analysis parameters are also provided.
The software is based of SUNDIALS, The Insight Toolkit, libxml2, and Boost C++.
The authors have created a very good open science publication. Source code is provided along with one set test of images and input analysis parameters.
The work is based on open source software, which also is helpful. It was noted that SUNDIALS does not have a direct source download, which was a minor impediment.
Reproducibility:I was able to build their code and run the application on the given test data. The analysis ran quickly.
I did not generate the visualizations presented in the article -- it would have been nice for the code to create these was provided also.
I created a Docker image [1] [2] to build and run the code. This work was presented as an example of a good open science publication at the 2014 IEEE NSS-MIC conference [3].
[1] https://github.com/thewtex/docker-itkka
[2] https://registry.hub.docker.com/u/thewtex/itkka/
[3] https://github.com/thewtex/ieee-nss-mic-scipy-2014
Use of Open Source Software:More discussion of their experiences with open source software could be useful.
Open source Contributions:The code was well cared for and built without issue according to the instructions provided.
It took some time to build the code and its dependencies. In the end, the full list of steps required can be found in the published Dockerfile [1].
[1] https://github.com/thewtex/docker-itkka/blob/master/Dockerfile
Code Quality :The code is generally high quality. More work could be done to improve the style, consistency, and readability.
There does not appear to be non-portable code, but this was not tested.
Realistic data was provided. A few more datasets could be useful.
Interest:This is a very useful library for those wishing to fix kinetic models to their data based on high quality, open science code.
Free comment :Thank you for excellent contribution.
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Version 1.3 of the itkka library now available via git:
https://bitbucket.csiro.au/projects/MILX/repos/itkka-pub
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Paper Id: | 924 |
Categories: | Image, Optimization |
Keywords: | Kinetic Analysis, Positron Emission Tomography, Magnetic Resonance, PET, MRI, Compartment Model |
Tracking Number: | NHMRC 631567, Queensland Cancer Council |
Toolkits: | ITK |
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