BrainAGE Designer

Brain Age Gap Estimation 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 3.8 or later
• MongoDB 3.6 or later
• Matlab Runtime v93 (optional)

Download

Using the git command-line tool:

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 and extract it.

Running on localhost

# 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

Start server and worker:

./start-server.sh

visit 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:

# 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 or the Docker Desktop if you can't help it.

Ubuntu 18.04

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 to docker-compose.yml and replace the <PATH-TO-...> entries:

<PATH-TO-DATA>:   the top-most directory where all data read and written to
<PATH-TO-MATLAB>: the directory of the matlab (v93 / R2017) runtime
<PATH-TO-CAT12>:  the directory of the CAT12 standalone version

docker compose build
docker compose up

and visit http://localhost.

run single docker images

# ./build-frontend.sh

docker build --tag brainage-designer .
docker run -ti -p 80:9009 brainage-designer

Development

prepare environments

# 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:

# transpile with yarn & parcel
./build-frontend.sh
# start the python server
./start-server.sh

and visit http://localhost:9009.

run server on localhost with hot-reloading

In project root:

# start the python server
./start-server.sh

In another shell in frontend directory:

yarn start

and visit http://localhost:1234.