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Fabian Peter Hammerle 111c081c3a added abstract class VolumeFile		5 лет назад
examples	8bfbe75024 move/rename read_hippocampal_volume_file_dataframe -> freesurfer.HippocampalSubfieldsVolumeFile.read_volumes_dataframe()	5 лет назад
freesurfer_volume_reader	111c081c3a added abstract class VolumeFile	5 лет назад
tests	5eb2727163 fix pylint similarity warning	5 лет назад
.gitignore	5af1308d8e git ignore build/ & dist/	5 лет назад
.pylintrc	07b02d4e5b pylint: disable missing-docstring	5 лет назад
.travis.yml	9f97bd4982 travis-ci: exclude pandas-version<=0.23 && python>=3.7 due to compile error	5 лет назад
Pipfile	8fd97e7d69 added failing test covering invalid root path '/'	5 лет назад
Pipfile.lock	8fd97e7d69 added failing test covering invalid root path '/'	5 лет назад
README.md	8bfbe75024 move/rename read_hippocampal_volume_file_dataframe -> freesurfer.HippocampalSubfieldsVolumeFile.read_volumes_dataframe()	5 лет назад
setup.py	276b501c93 split __main__.py from __init__.py	5 лет назад

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

freesurfer-volume-reader /my/freesurfer/subjects
freesurfer-volume-reader /my/freesurfer/subjects /other/freesurfer/subjects

from freesurfer_volume_reader.freesurfer import HippocampalSubfieldsVolumeFile

for volume_file in HippocampalSubfieldsVolumeFile.find('/my/freesurfer/subjects'):
    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

README.md

freesurfer-volume-reader

Install

Usage

Tests