Installation

Install dcm2niix

To use phantom_check, first install dcm2niix and add it to PATH variable.

export PATH=${PATH}:/PATH/TO/DCM2NIIX
echo "export PATH=${PATH}:/PATH/TO/DCM2NIIX" > ~/.bashrc

Install heudiconv

heudiconv is also required to run phantom_check. Install heudiconv following the instruction on their website, and make sure you can access heudiconv from your console.

heudiconv -h

Install phantom_check

Install from pip

pip install phantom_check

or install from github

git clone https://github.com/AMP-SCZ/phantom_check
cd phantom_check

pip install heudiconv[all]  #installing heudiconv
pip install -r requirements.txt

Note

if you used git to clone phantom_check, add the script path to your ~/.bashrc

echo "export PATH=${PATH}:~/phantom_check/scripts" >> ~/.bashrc