freesurfer-volume-reader ======================== .. image:: https://travis-ci.org/fphammerle/freesurfer-volume-reader.svg?branch=master :target: https://travis-ci.org/fphammerle/freesurfer-volume-reader .. image:: https://coveralls.io/repos/github/fphammerle/freesurfer-volume-reader/badge.svg?branch=master :target: https://coveralls.io/github/fphammerle/freesurfer-volume-reader?branch=master .. image:: https://img.shields.io/pypi/v/freesurfer-volume-reader.svg :target: https://pypi.org/project/freesurfer-volume-reader/#history .. image:: https://img.shields.io/pypi/pyversions/freesurfer-volume-reader.svg :target: https://pypi.org/project/freesurfer-volume-reader/ .. image:: https://zenodo.org/badge/183625692.svg :target: https://zenodo.org/badge/latestdoi/183625692 Python script & library to read hippocampal subfield volumes computed by Freesurfer & ASHS - Freesurfer https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields - ASHS https://sites.google.com/site/hipposubfields/home Install ------- .. code:: sh pip3 install --user freesurfer-volume-reader freesurfer-volume-reader --help Releases follow the `semantic versioning `__ scheme. Usage ----- Freesurfer ~~~~~~~~~~ .. code:: sh export SUBJECTS_DIR=/my/freesurfer/subjects freesurfer-volume-reader or .. code:: sh freesurfer-volume-reader /my/freesurfer/subjects freesurfer-volume-reader /my/freesurfer/subjects /other/freesurfer/subjects or .. code:: python 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 ~~~~ .. code:: sh export SUBJECTS_DIR=/my/ashs/subjects freesurfer-volume-reader --source-types ashs or .. code:: sh freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects /other/ashs/subjects or .. code:: python 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()) Intracranial Volume ^^^^^^^^^^^^^^^^^^^ .. code:: python from freesurfer_volume_reader import ashs for volume_file in ashs.IntracranialVolumeFile.find('/my/ashs/subjects'): print(volume_file.subject) print(volume_file.read_volume_mm3()) print(volume_file.read_volume_series()) Freesurfer & ASHS ~~~~~~~~~~~~~~~~~ .. code:: sh 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 ----- .. code:: sh 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