Fabian Peter Hammerle
6882ef0878
fix indeterministic integration test: sort rows before comparison
|
преди 5 години | |
|---|---|---|
| freesurfer_volume_reader | преди 5 години | |
| tests | преди 5 години | |
| .pylintrc | преди 5 години | |
| .travis.yml | преди 5 години | |
| Pipfile | преди 5 години | |
| Pipfile.lock | преди 5 години | |
| README.md | преди 5 години | |
| setup.py | преди 5 години |
README.md
freesurfer-volume-reader
Python script & library to read hippocampal subfield volumes computed by Freesurfer
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
Install
pip3 install --user freesurfer-volume-reader
freesurfer-volume-reader --help
Usage
export SUBJECTS_DIR=/my/freesurfer/subjects
freesurfer-volume-reader
or
freesurfer-volume-reader /my/freesurfer/subjects
or
from freesurfer_volume_reader import find_hippocampal_volume_files, \
read_hippocampal_volume_file_dataframe
for volume_file_path in find_hippocampal_volume_files('/my/freesurfer/subjects'):
print(read_hippocampal_volume_file_dataframe(volume_file_path))
Tests
pip3 install --user pipenv
git clone https://github.com/fphammerle/freesurfer-volume-reader.git
cd freesurfer-volume-reader
pipenv run pylint freesurfer_volume_reader
pipenv run pytest