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Fabian Peter Hammerle c2c741e339 move/rename parse_hippocampal_volume_file_path() -> freesurfer.HippocampalSubfieldsVolumeFile.__init__() 6 lat temu
examples c2c741e339 move/rename parse_hippocampal_volume_file_path() -> freesurfer.HippocampalSubfieldsVolumeFile.__init__() 6 lat temu
freesurfer_volume_reader c2c741e339 move/rename parse_hippocampal_volume_file_path() -> freesurfer.HippocampalSubfieldsVolumeFile.__init__() 6 lat temu
tests c2c741e339 move/rename parse_hippocampal_volume_file_path() -> freesurfer.HippocampalSubfieldsVolumeFile.__init__() 6 lat temu
.gitignore 5af1308d8e git ignore build/ & dist/ 6 lat temu
.pylintrc 07b02d4e5b pylint: disable missing-docstring 6 lat temu
.travis.yml 9f97bd4982 travis-ci: exclude pandas-version<=0.23 && python>=3.7 due to compile error 6 lat temu
Pipfile 8fd97e7d69 added failing test covering invalid root path '/' 6 lat temu
Pipfile.lock 8fd97e7d69 added failing test covering invalid root path '/' 6 lat temu
README.md c2c741e339 move/rename parse_hippocampal_volume_file_path() -> freesurfer.HippocampalSubfieldsVolumeFile.__init__() 6 lat temu
setup.py f00fbdee19 setup.py: fix description (1 line only), added long description 6 lat temu

README.md

freesurfer-volume-reader

Build Status

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.freesurfer import HippocampalSubfieldsVolumeFile
from freesurfer_volume_reader import read_hippocampal_volume_file_dataframe

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

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