brainweb-dl 0.0.1

Download BrainWeb MRI data

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.

Get Started

Data Location

The cached data directory follows this priority order:

1. User-specific argument (brainweb_dir in most functions)
2. BRAINWEB_DIR environment variable
3. ~/.cache/brainweb folder

Python Script Usage

from brainweb_dl import get_mri 

data = get_mri(subject=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 [e-mail]/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.
• Introduce an interface to download as BIDS format.
• 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).

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.

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