Residual and Plain Convolutional Neural Networks for 3D Brain MRI Classification

https://arxiv.org/abs/1701.06643

Authors: Sergey Korolev, Amir Safiullin, Mikhail Belyaev, Yulia Dodonova

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Scripts for training without Docker image are located in scripts folder

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Install docker-jupyter

Install Docker https://docs.docker.com/engine/installation/

Install nvidia-docker https://github.com/NVIDIA/nvidia-docker/wiki/Installation

Howto run docker-jupyter

Clone:

git clone https://github.com/neuro-ml/resnet_cnn_mri.git

cd resnet_cnn_mri

Build:

[sudo] docker build -t dl_isbi:repr -f Dockerfile .

Run container:

[sudo] nvidia-docker run -it -p 8809:8888 -v ~/absolute/path/to_data:/scripts/data/ dl_isbi:repr bash

where ~/absolute/path/to_data is absolute path on your local machine to folder with adni data.

Run notebook inside the container:

jupyter notebook

Open http://localhost:8809 on your local machine.

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Data

Place all the .nii files and metadata.csv inside ~/absolute/path/to_data (on your local machine).

metadata.csv should have Label and Path columns for file retrieval and class labels (you can find sample /scripts/data/metadata.csv). Path value shoult be data/some/path/to_scan.nii