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+freesurfer-volume-reader
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+========================
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+
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+.. image:: https://travis-ci.org/fphammerle/freesurfer-volume-reader.svg?branch=master
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+ :target: https://travis-ci.org/fphammerle/freesurfer-volume-reader
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+.. image:: https://coveralls.io/repos/github/fphammerle/freesurfer-volume-reader/badge.svg?branch=master
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+ :target: https://coveralls.io/github/fphammerle/freesurfer-volume-reader?branch=master
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+.. image:: https://img.shields.io/pypi/v/freesurfer-volume-reader.svg
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+ :target: https://pypi.org/project/freesurfer-volume-reader/#history
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+.. image:: https://img.shields.io/pypi/pyversions/freesurfer-volume-reader.svg
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+ :target: https://pypi.org/project/freesurfer-volume-reader/
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+
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+Python script & library to read hippocampal subfield volumes computed by
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+Freesurfer & ASHS
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+
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+- Freesurfer
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+ https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
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+- ASHS https://sites.google.com/site/hipposubfields/home
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+
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+Install
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+-------
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+
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+.. code:: sh
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+
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+ pip3 install --user freesurfer-volume-reader
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+ freesurfer-volume-reader --help
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+
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+Releases follow the `semantic versioning <https://semver.org/>`__
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+scheme.
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+
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+Usage
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+-----
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+
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+Freesurfer
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+~~~~~~~~~~
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+
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+.. code:: sh
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+
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+ export SUBJECTS_DIR=/my/freesurfer/subjects
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+ freesurfer-volume-reader
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+
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+or
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+
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+.. code:: sh
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+
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+ freesurfer-volume-reader /my/freesurfer/subjects
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+ freesurfer-volume-reader /my/freesurfer/subjects /other/freesurfer/subjects
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+
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+or
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+
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+.. code:: python
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+
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+ from freesurfer_volume_reader import freesurfer
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+
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+ for volume_file in freesurfer.HippocampalSubfieldsVolumeFile.find('/my/freesurfer/subjects'):
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+ print(volume_file.subject, volume_file.hemisphere, volume_file.analysis_id)
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+ print(volume_file.read_volumes_mm3())
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+ print(volume_file.read_volumes_dataframe())
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+
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+ASHS
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+~~~~
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+
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+.. code:: sh
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+
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+ export SUBJECTS_DIR=/my/ashs/subjects
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+ freesurfer-volume-reader --source-types ashs
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+
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+or
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+
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+.. code:: sh
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+
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+ freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects
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+ freesurfer-volume-reader --source-types ashs -- /my/ashs/subjects /other/ashs/subjects
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+
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+or
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+
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+.. code:: python
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+
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+ from freesurfer_volume_reader import ashs
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+
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+ for volume_file in ashs.HippocampalSubfieldsVolumeFile.find('/my/ashs/subjects'):
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+ print(volume_file.subject, volume_file.hemisphere, volume_file.correction)
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+ print(volume_file.read_volumes_mm3())
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+ print(volume_file.read_volumes_dataframe())
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+
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+Intracranial Volume
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+^^^^^^^^^^^^^^^^^^^
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+
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+.. code:: python
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+
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+ from freesurfer_volume_reader import ashs
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+
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+ for volume_file in ashs.IntracranialVolumeFile.find('/my/ashs/subjects'):
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+ print(volume_file.subject)
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+ print(volume_file.read_volume_mm3())
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+ print(volume_file.read_volume_series())
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+
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+Freesurfer & ASHS
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+~~~~~~~~~~~~~~~~~
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+
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+.. code:: sh
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+
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+ freesurfer-volume-reader --source-types ashs freesurfer-hipposf -- /my/subjects
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+ freesurfer-volume-reader --source-types ashs freesurfer-hipposf -- /my/ashs/subjects /my/freesurfer/subjects /other/subjects
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+
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+Tests
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+-----
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+
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+.. code:: sh
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+
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+ pip3 install --user pipenv
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+ git clone https://github.com/fphammerle/freesurfer-volume-reader.git
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+ cd freesurfer-volume-reader
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+ pipenv run pylint freesurfer_volume_reader
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+ pipenv run pytest
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