https://github.com/netzkolchose/brainage-designer
BrainAGE (Brain Age Gap Estimation) framework with browser interface
https://github.com/netzkolchose/brainage-designer
age-estimation brainage machine-learning mri-images web-ui
Last synced: about 1 year ago
JSON representation
BrainAGE (Brain Age Gap Estimation) framework with browser interface
- Host: GitHub
- URL: https://github.com/netzkolchose/brainage-designer
- Owner: netzkolchose
- Created: 2023-11-08T14:21:15.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2023-11-17T12:52:54.000Z (over 2 years ago)
- Last Synced: 2025-01-31T13:43:45.789Z (over 1 year ago)
- Topics: age-estimation, brainage, machine-learning, mri-images, web-ui
- Language: Python
- Homepage:
- Size: 5.82 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# BrainAGE Designer
[](https://github.com/defgsus/brainage-designer/actions/workflows/tests.yml)
[](https://github.com/defgsus/brainage-designer/actions/workflows/build-frontend-main.yml)
**Brain** **A**ge **G**ap **E**stimation framework with browser-based user interface.
Some of the features:
- all experiments are controlled from the web-UI
- supports arbitrary preprocessing pipelines
- fine control over analysis / model creation
- all experiments are stored to database for revisiting them later
## Installation
### Requirements
- [Python](https://www.python.org/) 3.8 or later
- [MongoDB](https://www.mongodb.com/) 3.6 or later
- [Matlab Runtime](https://www.mathworks.com/products/compiler/matlab-runtime.html) v93 (optional)
### Download
Using the git command-line tool:
```shell
cd /my/projects # or where you want to place it
git clone https://github.com/defgsus/brainage-designer.git
cd brainage-designer
git checkout development-frontend
```
or you can download [a zip file](https://github.com/defgsus/brainage-designer/archive/refs/heads/development-frontend.zip)
and extract it.
### Running on localhost
```shell
# create new python environment
python -m venv env
# activate
source env/bin/activate
# install python packages
pip install -r requirements.txt
pip install https://github.com/JamesRitchie/scikit-rvm/archive/master.zip
```
[Install MongoDB](https://www.mongodb.com/docs/manual/installation/)
Start server and worker:
```shell
./start-server.sh
```
visit [http://localhost:9009](http://localhost:9009)
#### Configuration
The local setup can be configure by creating a `.env` file
in the root directory. It can have the following entries:
```shell
# enable debugging mode (mainly for web-server, more text output)
BAD_DEBUG=true
# -- directories --
# the root path below which everything can be accessed
BAD_DATA_PATH=/home/me
# temporary directory to use
TEMP_PATH=/tmp/brainage-designer
# -- matlab --
# path to the matlab runtime
MATLAB_PATH=/home/me/MATLAB_Runtime/v93
# path to the matlab-based CAT12 toolbox
CAT12_PATH=/home/me/CAT12.8.1_r2042_R2017b_MCR_Linux
# -- API server --
# change the address of the API (and frontend) server
SERVER_HOST=localhost
SERVER_PORT=9009
# -- mongodb --
# rename the database
DATABASE_NAME=brainage-designer
# location of the mongodb server
DATABASE_HOST=localhost
DATABASE_PORT=27017
# to handle authentication with mongodb
DATABASE_USER=brainage-user
DATABASE_PASSWORD=brainage-password
```
## Installation via 'Docker'
Install a recent version of [Docker Engine](https://docs.docker.com/engine/install/)
or the **Docker Desktop** if you can't help it.
#### Ubuntu 18.04
```shell
mkdir tmp
cd tmp
wget https://download.docker.com/linux/ubuntu/dists/bionic/pool/stable/amd64/containerd.io_1.6.9-1_amd64.deb
wget https://download.docker.com/linux/ubuntu/dists/bionic/pool/stable/amd64/docker-ce-cli_20.10.9~3-0~ubuntu-bionic_amd64.deb
wget https://download.docker.com/linux/ubuntu/dists/bionic/pool/stable/amd64/docker-ce_20.10.9~3-0~ubuntu-bionic_amd64.deb
wget https://download.docker.com/linux/ubuntu/dists/bionic/pool/stable/amd64/docker-compose-plugin_2.6.0~ubuntu-bionic_amd64.deb
sudo dpkg -i *.deb
cd ..
rm -r tmp/
```
### run with docker compose
Copy the file [docker-compose-EXAMPLE.yml](docker-compose-EXAMPLE.yml) to `docker-compose.yml` and
replace the `` entries:
: the top-most directory where all data read and written to
: the directory of the matlab (v93 / R2017) runtime
: the directory of the CAT12 standalone version
```shell
docker compose build
docker compose up
```
and visit [http://localhost](http://localhost).
### run single docker images
```shell
# ./build-frontend.sh
docker build --tag brainage-designer .
docker run -ti -p 80:9009 brainage-designer
```
# Development
### prepare environments
```shell
# for python the typical..
python -m venv env
source env/bin/activate
pip install -r requirements.txt
# for frontend
cd frontend
yarn
```
### run server on localhost
In project root:
```shell
# transpile with yarn & parcel
./build-frontend.sh
# start the python server
./start-server.sh
```
and visit [http://localhost:9009](http://localhost:9009).
### run server on localhost with hot-reloading
In project root:
```shell
# start the python server
./start-server.sh
```
In another shell in `frontend` directory:
```shell
yarn start
```
and visit [http://localhost:1234](http://localhost:1234).