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CCSegThickness

Software Pipeline for Midsagittal Corpus Callosum Thickness Profile Processing

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:

  1. Midsagittal plane extraction
  2. CC segmentation algorithm - Automated Segmentation
  3. Quality control tool - Manual Editor
  4. Thickness profile generation
  5. Statistical analysis - Group-Wise Statistical Comparison
  6. Results figure generator - Results Display

Installation

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