Quick start

nifti-snapshot is a tool to quickly capture nifti image as a png or jpg figures.

Install the nifti-snapshot

Install nifti-snapshot using pip

pip install nifti_snapshot

Note

It’s _, not -

For the most recent version of nifti_snapshot, pull the most recent master branch from github repository.

git clone https://github.com/pnlbwh/nifti-snapshot

ENIGMA nifti data

Download ENIGMA data

nifti-snapshot requires nifti maps that ENIGMA published. It can be downlaoded by executing the command below.

enigma_data_dir=${HOME}/enigma_data   # change this if you want to
mkdir -p ${enigma_data_dir}
wget http://enigma.ini.usc.edu/wp-content/uploads/2013/02/enigmaDTI.zip -P ${enigma_data_dir}
unzip -o -d ${enigma_data_dir} ${enigma_data_dir}/enigmaDTI.zip

Set up PATH environment

Add below line to your bashrc (~/.bashrc) or execute it everytime you use nifti-snapshot.

echo "export enigma_data_dir=${HOME}/enigma_data" >> ~/.bashrc   # change this if you want to
source ~/.bashrc

Check installation

nifti_snapshot -h
nifti_snapshot --check_enigma

Note

If you have downloaded nifti-snapshot from its github repository, you will also have to add path of the nifti_snapshot/script to your PATH and nifti_snapshot/nifti_snapshot to your PYTHONPATH variable to access nifti_snapshot executable from any location.

export PYTHONPATH=${PATH}:${HOME}/nifti_snapshot/nifti_snapshot
export PATH=${PATH}:${HOME}/nifti_snapshot/script

Test create an image

nifti_snapshot \
    --input ${enigma_data_dir}/ENIGMA_DTI_FA.nii.gz \
    --title test_title \
    --output_file t1w_test.png

Congratulations!