Metadata-Version: 1.1
Name: mrainet
Version: 0.1.0
Summary: MR acquisition-invariant network.
Home-page: https://github.com/wmkouw/mrai-net
Author: Wouter Kouw
Author-email: wmkouw@gmail.com
License: Apache 2.0
Description: [![Coverage](https://scrutinizer-ci.com/g/wmkouw/mrai-net/badges/coverage.png?b=master)](https://scrutinizer-ci.com/g/wmkouw/mrai-net/statistics/)
        [![BuildStatus](https://travis-ci.org/wmkouw/mrai-net.svg?branch=master)](https://travis-ci.org/wmkouw/mrai-net) [![Docs](https://media.readthedocs.org/static/projects/badges/passing-flat.svg)](https://mrai-net.readthedocs.io/en/latest/index.html) ![Python version](https://img.shields.io/badge/python-3.5%2C%203.6-blue.svg) [![DOI](https://zenodo.org/badge/95411302.svg)](https://zenodo.org/badge/latestdoi/95411302)
        
        # MR Acquisition-Invariant Neural Network
        
        This repository contains experiments and code accompanying the paper:
        
        "MR Acquisition-Invariant Representation Learning"
        
        which is currently under review. The preprint is on [ArXiv](https://arxiv.org/abs/1709.07944).
        
        ## Installation
        
        mrainet can be installed through:
        ```shell
        pip install mrainet
        ```
        
        PyPI takes care of all dependencies. However, to ensure that these don't mess up your current python environment, you should set up a virtual one. If you're familiar with [conda](https://conda.io/docs/), you can do this through:
        ```
        conda env create -f environment.yml
        source activate mrainet
        ```
        
        ## Usage
        
        Please visit the [examples](https://mrai-net.readthedocs.io/en/latest/examples.html) section in the documentation to get started.
        
        To give you an impression of how the module is used, here's an example call:
        ```python
        from mrainet.mraicnn import MRAIConvolutionalNeuralNetwork
        
        M = MRAIConvolutionalNeuralNetwork()
        M.train(X,Y,Z,U)
        
        H = M.feedforward(X)
        ```
        where X are MRI-scans from the source scanner, Y are their corresponding segmentations, Z are MRI-scans from the target scanner, and U is its corresponding incomplete segmentations (nearly all are NaN). H represents the patches fed through the network and embedded in MRAI-net's penultimate layer (MRAI representation).
        
        For more information on individual classes, methods and functions, visit the [docs](https://mrai-net.readthedocs.io/en/latest/).
        
        ## Data
        
        In order to isolate MRI-scanner acquisition-based variation in medical images, we simulated datasets of varying scan protocol parameters using [SIMRI](https://www.ncbi.nlm.nih.gov/pubmed/15705518). High-quality human brain phantoms were used, which can be found here:
        - [Brainweb](http://brainweb.bic.mni.mcgill.ca/)
        
        
        The original code for SIMRI can be downloaded from [here](https://sourceforge.net/projects/simri/). Our repo contains a modified version of SIMRI that includes the additional NMR relaxation times, as described in the paper's appendix. For more information on how to run your own simulations, see the example shell script named `run_simulation.sh` in the folder `data/brainweb/simulator`.
        
        Real data consisted of the MRBrainS data set, known from the brain tissue segmentation challenge at MICCAI 2013.
        - [MRBrainS](http://mrbrains13.isi.uu.nl/)
        
        We used only the 5 training scans provided, as the labels for the remaining 15 scans have not been released.
        
        ## Experiments
        
        Experimental scripts from the paper are included in this repository:
        - `exp-mrai-cnn_b1b3`: simulated data from MRI-scanners with different acquisition protocols.
        - `exp_mrai-cnn_b1mb`: simulated data as souce and real data as target, for different field strengths.
        - `exp_mrai-cnn_b3mb`: simulated data as souce and real data as target, for equivalent field strengths.
        
        For more information on experiment parameters and setup, see the [README](https://github.com/wmkouw/mrai-net/tree/master/experiments) in the experiments folder.
        
        ## Contact
        Bugs, comments and questions can be submitted to the [issues tracker](https://github.com/wmkouw/mrai-net/issues).
        
Platform: UNKNOWN
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Scientific/Engineering :: Image Recognition
Classifier: License :: OSI Approved :: MIT License
Classifier: Development Status :: 3 - Alpha
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
