CCSegThickness performs fully automated pipeline for thickness profile evaluation and analysis of the human corpus callosum (CC) in 3D structural T1-weighted magnetic resonance images
The pipeline performs the following sequence of steps:
- Midsagittal plane extraction
- CC segmentation algorithm - Automated Segmentation
- Quality control tool - Manual Editor
- Thickness profile generation
- Statistical analysis - Group-Wise Statistical Comparison
- Results figure generator - Results Display
Tested in Ubuntu 16.04 LTS, 18.04 LTS.
git clone https://github.com/chrisadamsonmcri/CCSegThickness
The following packages are dependencies and need to be installed via apt
sudo apt install python3-dev python3-pip python3-numpy python3-scipy python3-nibabel python3-opencv python3-imageio python3-matplotlib libsuitesparse-dev cython3
The following package needs to be installed in pip
sudo -H pip3 install -U scikits.sparse
These installations can be done with the script
install_dependencies.sh
Finally, make the streamline cython file
cd CCSegThickness
./make_cython.sh
If you use the software in a publication, please cite the following article:
Adamson, C., Beare, R., Walterfang, M. et al. Neuroinform (2014) 12: 595. https://doi.org/10.1007/s12021-014-9236-3