Fabian Peter Hammerle
7879965c6e
setup.py: added classifiers
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| examples | %!s(int64=5) %!d(string=hai) anos | |
| freesurfer_volume_reader | %!s(int64=5) %!d(string=hai) anos | |
| tests | %!s(int64=5) %!d(string=hai) anos | |
| .pylintrc | %!s(int64=5) %!d(string=hai) anos | |
| .travis.yml | %!s(int64=5) %!d(string=hai) anos | |
| Pipfile | %!s(int64=5) %!d(string=hai) anos | |
| Pipfile.lock | %!s(int64=5) %!d(string=hai) anos | |
| README.md | %!s(int64=5) %!d(string=hai) anos | |
| setup.py | %!s(int64=5) %!d(string=hai) anos |
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