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freesurfer-volume-reader
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Fabian Peter Hammerle 0936faaed8 Merge branch 'semantic-versioning' 5 år sedan
examples 1abafc1ed8 test `python -m` module call to increase coverage 5 år sedan
freesurfer_volume_reader 4b7481f697 version.py: rename version string variable `version` -> `__version__` to fix pylint C0103 5 år sedan
tests 06250eee7c script: added flag `--version` 5 år sedan
.coveragerc 6b2c883982 coverage: enable branch management 5 år sedan
.gitignore 904501c765 set module version string via setuptools_scm's `write_to` option 5 år sedan
.pylintrc 0ca4226d54 added ashs.HippocampalSubfieldsVolumeFile.read_volumes_mm3() 5 år sedan
.travis.yml 0a098ce5d1 travis-ci: fail if coverage < 100% 5 år sedan
Pipfile 863bbde9ed set upper version constraint for dependencies to prevent unexpected breaking changes 5 år sedan
Pipfile.lock 863bbde9ed set upper version constraint for dependencies to prevent unexpected breaking changes 5 år sedan
README.md eb9058a5c6 readme: added note on semantic versioning of releases 5 år sedan
setup.py 4b7481f697 version.py: rename version string variable `version` -> `__version__` to fix pylint C0103 5 år sedan

README.md

freesurfer-volume-reader

Build Status

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