Download BrainWeb MRI data
Project description
Brainweb-DL
Welcome to Brainweb-DL, a powerful Python toolkit for downloading and converting the Brainweb dataset.
Features
-
Effortless Dataset Management: Automatically download, cache, and format the Brainweb dataset with ease. Convert it to the convenient nifti format or numpy array hassle-free.
-
Multiple Image Generation: Generate high-quality T1, T2, T2*, and PD images directly from the Brainweb dataset. Perfect for testing purposes, although keep in mind that the values provided are approximate.
Available data
The Brainweb project kindly provides:
- A normal brain phantom (named subject
0
afterwards), with T1, T2 and PD contrasts, with a variety of noise levels and intensity non-uniformities. As well as a anatomical model (in the form of either crisp or fuzzy segmentation of brain tissues, at a fixed resolution of 181x217x181 images). - The same for a multiple sclerosis brain phantom (named subject
1
afterwards). - A set of 20 normal brains (with ids equal to
[4, 5, 6, 18, 20, 38, 41-54]
) , with a T1 contrast (with 1mm resolution at (181, 217,181)), as well as the crisp and fuzzy segmentation of brain tissues (with a shape of (362, 434,362)) [^1].
This project provides a CLI and a Python API to download and convert theses data. On top of that, it can generate new contrasts (e.g. T2*) from the segmentations, and reshape the data to the desired resolution [^2].
[^1]: Note that the classification of tissue is not the same as for subject 0 and 1 [^2]: This requires scipy to be installed.
Get Started
Data Location
The cached data directory follows this priority order:
- User-specific argument (
brainweb_dir
in most functions) BRAINWEB_DIR
environment variable~/.cache/brainweb
folder
Python Script Usage
from brainweb_dl import get_mri
data = get_mri(sub_id=44, contrast="T1")
The Brainweb dataset is downloaded and cached by default in the ~/.cache/brainweb
folder.
Command Line Interface
brainweb-dl 44 --contrast=T1
For more information, see brainweb-dl --help
.
Installation
Get up and running quickly!
pip install brainweb-dl
Development
Join our community and contribute to Brainweb-DL!
git clone git@github.com/paquiteau/brainweb-dl
cd brainweb-dl
pip install -e .[dev,test,doc]
TODO List
Help us improve and shape the future of Brainweb-DL:
- Add unit tests.
- Implement fuzzy search and multiple subjects download in parallel.
- Develop an interface to generate T1, T2, T2*, and PD images.
- Enhance the search for the location of the Brainweb dataset (User > Environment Variable > Default Location).
- Introduce an interface to download as BIDS format.
Acknowledgement
We extend our gratitude to the following for their contributions:
-
Casper De Clercq for the preliminary work and original idea. Check out his great work if you are interested in PET imaging and registration functionalities.
-
BrainWeb for providing this valuable dataset to the community.
:star2: If you like this work, don't forget to star it and share it 🌟
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