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Fabian Peter Hammerle 61180f2674 added ashs.IntracranialVolumeFile.read_volume_mm3() il y a 4 ans
examples d28cc369b0 breaking: rename class VolumeFile -> SubfieldVolumeFile il y a 4 ans
freesurfer_volume_reader 61180f2674 added ashs.IntracranialVolumeFile.read_volume_mm3() il y a 4 ans
tests 61180f2674 added ashs.IntracranialVolumeFile.read_volume_mm3() il y a 4 ans
.coveragerc 6b2c883982 coverage: enable branch management il y a 5 ans
.gitignore 62306616b0 examples pipenv: added jupyter notebook il y a 5 ans
.pylintrc 0ca4226d54 added ashs.HippocampalSubfieldsVolumeFile.read_volumes_mm3() il y a 5 ans
.travis.yml 6d0b5d6766 travis-ci: send coverage report to coveralls il y a 5 ans
Pipfile 863bbde9ed set upper version constraint for dependencies to prevent unexpected breaking changes il y a 5 ans
Pipfile.lock 863bbde9ed set upper version constraint for dependencies to prevent unexpected breaking changes il y a 5 ans
README.md af2779afe8 readme: added badge showing latest version released on pypi il y a 5 ans
setup.py 4b7481f697 version.py: rename version string variable `version` -> `__version__` to fix pylint C0103 il y a 5 ans

README.md

freesurfer-volume-reader

Build Status Coverage Status Latest PyPI Version Python Versions

Python script & library to read hippocampal subfield volumes computed by Freesurfer & ASHS

Install

pip3 install --user freesurfer-volume-reader
freesurfer-volume-reader --help

Releases follow the semantic versioning scheme.

Usage

Freesurfer

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

export SUBJECTS_DIR=/my/ashs/subjects
freesurfer-volume-reader --source-types ashs

or

freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects
freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects /other/ashs/subjects

or

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())

Freesurfer & ASHS

freesurfer-volume-reader --source-types ashs freesurfer-hipposf -- /my/subjects
freesurfer-volume-reader --source-types ashs freesurfer-hipposf -- /my/ashs/subjects /my/freesurfer/subjects /other/subjects

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