freesurfer-stats

freesurfer-stats
================

TODO add badges

Python Library to Read FreeSurfer's cortical parcellation anatomical statistics

Freesurfer https://surfer.nmr.mgh.harvard.edu/

Install
-------

.. code:: sh

pip3 install --user freesurfer-stats

Releases follow the `semantic versioning ` scheme.

Usage
-----

.. code:: python

>>> from freesurfer_stats import CorticalParcellationStats
>>> stats = CorticalParcellationStats.read('tests/subjects/fabian/stats/lh.aparc.DKTatlas.stats')
>>> stats.headers['CreationTime'].isoformat()
'2019-05-09T21:05:54+00:00'
>>> stats.headers['cvs_version']
'Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp'
>>> stats.headers['cmdline'][:64]
'mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label'
>>> stats.hemisphere
'left'
>>> stats.whole_brain_measurements['Estimated Total Intracranial Volume']
(1670487.274486, 'mm^3')
>>> stats.whole_brain_measurements['White Surface Total Area']
(98553.0, 'mm^2')
>>> stats.structure_measurements['postcentral']
{'Structure Name': 'postcentral',
'Number of Vertices': 8102,
'Surface Area': 5258.0,
'Gray Matter Volume': 12037.0,
'Average Thickness': 2.109,
'Thickness StdDev': 0.568,
...}
>>> stats.structure_measurement_units
{'Structure Name': None,
'Number of Vertices': None,
'Surface Area': 'mm^2',
'Gray Matter Volume': 'mm^3',
'Average Thickness': 'mm',
'Thickness StdDev': 'mm',
...}