/Preprocessing-Pipeline-on-Brain-MR-Images

The project is used to do preprocessing on brain MR images.

Primary LanguagePythonMIT LicenseMIT

Preprocessing Pipeline on Brain MR Images

Modify from a repository quqixun/BrainPrep.

The project is used to do preprocessing on brain MR images.

There is a pipeline include those features:

  • Auto AC-PC Detection
  • Registration
  • Skull Stripping
  • Segmentation

Requirements

All required libraries are listed as below:

  • tqdm
  • numpy
  • scipy
  • nipype
  • nibabel
  • matplotlib
  • scikit-learn
pip3 install -r requirement.txt

Usage

Download and Install Tools

  • Download and install FSL as instructions here from source code in Linux and macOS.
  • Compile /Compiling-ANTs-on-Linux-and-Mac-OS), or in Windows 10.
  • Download Auto AC-PC tools here into ./utils if you're not using MacOS.
  • Download ATRA tools in the same link here into ./utils if you're not using Linux-based system.

Download Dataset

See README.md in data.

The data can put in ./data, for example ./data/ADNI/T1.nii

Run the pipeline

python3 main.py

Results

results

Future

  • Multiprocessing
  • Clean code
  • ...