Metadata-Version: 1.1
Name: freesurfer-volume-reader
Version: 2.1.0
Summary: Python script & library to read hippocampal subfield volumescomputed by Freesurfer & ASHS
Home-page: https://github.com/fphammerle/freesurfer-volume-reader
Author: Fabian Peter Hammerle
Author-email: fabian@hammerle.me
License: UNKNOWN
Description: 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 <https://semver.org/>`__
        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
        
Keywords: brain,freesurfer,hippocampus,neuroimaging,reader,subfields
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Healthcare Industry
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Topic :: Utilities
