neuropoly/qmrlab repository overview

⁠What is qMRLab?

qMRLab⁠ is an open-source software for quantitative MR image analysis. The main goal is to provide the community with an intuitive tool for data fitting, plotting, simulation and protocol optimization for a myriad of different quantitative models.

⁠What is included in this image?

This image gives you all Command Line Interface (CLI) abilities of qMRLab on Jupyter Notebooks running SoS kernel⁠ that enables using multiple kernels in the same Notebook!

Octave installation has been manually configured to set a proper environment for image processing. Following Octave packages installed:

• general 2.0.0
• io 2.4.7
• control-3.0.0.tar.gz
• signal 1.3.2.tar.gz
• image 2.6.1.tar.gz
• struct 1.0.14.tar.gz
• optim 1.5.2.tar.gz
• statistics 1.3.0

You will also have the all functionality provided by jupyter/base-notebook⁠. On top of that, we've added Plotly⁠ to pave the way for a colorful and interactive qMRI analysis.

⁠Basic Use

1. Pull this image

docker pull neuropoly/qmrlab

1. The following command starts a container with the Notebook server listening for HTTP connections on port 8888 with a randomly generated authentication token configured.

docker run -it --rm -p 8888:8888 neuropoly/qmrlab

The last appearing line will be a URL that looks like this:

http://localhost:8888/?token=123456789123456789123456789123456789

1. Copy the generated token (1234...) to your clipboard and visit http://localhost:8888/ on your web browser. Paste token code and start using qMRLab on Jupyter Notebook.

⁠Online example: Fit MTsat

By clicking the BinderHub badge below, you can spin off our example notebook on your browser without pulling this image.

Sample data will be downloaded from qMRLab's OSF page⁠, a batch script will be generated to perform MTsat (Magnetization Transfer Saturation Index) fitting and executed.