# neuro

**Repository Path**: scitator/neuro

## Basic Information

- **Project Name**: neuro
- **Description**: Catalyst.Neuro
- **Primary Language**: Python
- **License**: Apache-2.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2020-09-16
- **Last Updated**: 2020-12-19

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

<div align="center">


[![Catalyst logo](https://raw.githubusercontent.com/catalyst-team/catalyst-pics/master/pics/catalyst_logo.png)](https://github.com/catalyst-team/catalyst)

**Accelerated DL R&D**

[![Build Status](http://66.248.205.49:8111/app/rest/builds/buildType:id:Catalyst_Deploy/statusIcon.svg)](http://66.248.205.49:8111/project.html?projectId=Catalyst&tab=projectOverview&guest=1)
[![CodeFactor](https://www.codefactor.io/repository/github/catalyst-team/catalyst/badge)](https://www.codefactor.io/repository/github/catalyst-team/catalyst)
[![Pipi version](https://img.shields.io/pypi/v/catalyst.svg)](https://pypi.org/project/catalyst/)
[![Docs](https://img.shields.io/badge/dynamic/json.svg?label=docs&url=https%3A%2F%2Fpypi.org%2Fpypi%2Fcatalyst%2Fjson&query=%24.info.version&colorB=brightgreen&prefix=v)](https://catalyst-team.github.io/catalyst/index.html)
[![PyPI Status](https://pepy.tech/badge/catalyst)](https://pepy.tech/project/catalyst)

[![Twitter](https://img.shields.io/badge/news-on%20twitter-499feb)](https://twitter.com/catalyst_core)
[![Telegram](https://img.shields.io/badge/channel-on%20telegram-blue)](https://t.me/catalyst_team)
[![Slack](https://img.shields.io/badge/Catalyst-slack-success)](https://join.slack.com/t/catalyst-team-core/shared_invite/zt-d9miirnn-z86oKDzFMKlMG4fgFdZafw)
[![Github contributors](https://img.shields.io/github/contributors/catalyst-team/catalyst.svg?logo=github&logoColor=white)](https://github.com/catalyst-team/catalyst/graphs/contributors)

</div>

PyTorch framework for Deep Learning research and development.
It was developed with a focus on reproducibility,
fast experimentation and code/ideas reusing.
Being able to research/develop something new,
rather than write another regular train loop. <br/>
Break the cycle - use the Catalyst!

Project [manifest](https://github.com/catalyst-team/catalyst/blob/master/MANIFEST.md). Part of [PyTorch Ecosystem](https://pytorch.org/ecosystem/). Part of [Catalyst Ecosystem](https://docs.google.com/presentation/d/1D-yhVOg6OXzjo9K_-IS5vSHLPIUxp1PEkFGnpRcNCNU/edit?usp=sharing):
- [Alchemy](https://github.com/catalyst-team/alchemy) - Experiments logging & visualization
- [Catalyst](https://github.com/catalyst-team/catalyst) - Accelerated Deep Learning Research and Development
- [Reaction](https://github.com/catalyst-team/reaction) - Convenient Deep Learning models serving

[Catalyst at AI Landscape](https://landscape.lfai.foundation/selected=catalyst).

---

# Catalyst.Neuro [![Build Status](https://travis-ci.com/catalyst-team/neuro.svg?branch=master)](https://travis-ci.com/catalyst-team/neuro) [![Github contributors](https://img.shields.io/github/contributors/catalyst-team/neuro.svg?logo=github&logoColor=white)](https://github.com/catalyst-team/neuro/graphs/contributors)

Developed in a partnership with

<div align="center">

[![Catalyst logo](https://raw.githubusercontent.com/catalyst-team/catalyst-pics/master/third_party_pics/TReNDS_logo.png)](https://trendscenter.org)

**Brain image analysis**

</div>

### How to run

You can reproduce MeshNet demo with 4 simple steps
- Install requirements
    ```bash
    pip install -r ./requirements/requirements.txt
    ```
- Download data via
    ```bash
    bash bin/download_dataset.sh
    ```
- Prepare data
    ```bash
    python neuro/scripts/prepare_data.py ./data/Mindboggle_101
    ```
- Start training (requires 64GB RAM due to data preprocessing)
    ```bash
    # for single GPU usage
    CUDA_VISIBLE_DEVICES=0 USE_APEX=0 catalyst-dl run --config=./training/configs/config.yml  --verbose
    # for multiGPU training
    CUDA_VISIBLE_DEVICES=0,2 USE_APEX=1 USE_DDP=1 catalyst-dl run --config=./training/configs/config.yml --verbose
    ```