Fabian Peter Hammerle
0d6cacdd34
Revert "configure pytest to always create coverage report"
|
5 年之前 | |
|---|---|---|
| examples | 5 年之前 | |
| freesurfer_volume_reader | 5 年之前 | |
| tests | 5 年之前 | |
| .gitignore | 5 年之前 | |
| .pylintrc | 5 年之前 | |
| .travis.yml | 5 年之前 | |
| Pipfile | 5 年之前 | |
| Pipfile.lock | 5 年之前 | |
| README.md | 5 年之前 | |
| setup.py | 5 年之前 |
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
freesurfer-volume-reader /my/freesurfer/subjects /other/freesurfer/subjects
or
from freesurfer_volume_reader import freesurfer
for volume_file in freesurfer.HippocampalSubfieldsVolumeFile.find('/my/freesurfer/subjects'):
print(volume_file.subject, volume_file.hemisphere, volume_file.analysis_id)
print(volume_file.read_volumes_mm3())
print(volume_file.read_volumes_dataframe())
ASHS
from freesurfer_volume_reader import ashs
for volume_file in ashs.HippocampalSubfieldsVolumeFile.find('/my/ashs/subjects'):
print(volume_file.subject, volume_file.hemisphere, volume_file.correction)
print(volume_file.read_volumes_mm3())
print(volume_file.read_volumes_dataframe())
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