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- freesurfer-stats
- ================
- .. image:: https://travis-ci.org/fphammerle/freesurfer-stats.svg?branch=master
- :target: https://travis-ci.org/fphammerle/freesurfer-stats
- .. image:: https://coveralls.io/repos/github/fphammerle/freesurfer-stats/badge.svg?branch=master
- :target: https://coveralls.io/github/fphammerle/freesurfer-stats?branch=master
- .. image:: https://img.shields.io/pypi/v/freesurfer-stats.svg
- :target: https://pypi.org/project/freesurfer-stats/#history
- .. image:: https://img.shields.io/pypi/pyversions/freesurfer-stats.svg
- :target: https://pypi.org/project/freesurfer-stats/
- 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 <https://semver.org/>` scheme.
- Usage
- -----
- .. code:: python
- >>> from freesurfer_stats import CorticalParcellationStats
- >>> stats = CorticalParcellationStats.read('tests/subjects/fabian/stats/lh.aparc.DKTatlas.stats')
- >>> stats.headers['subjectname']
- 'fabian'
- >>> 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_mm^3']
- 0 1.670487e+06
- Name: estimated_total_intracranial_volume_mm^3, dtype: float64
- >>> stats.whole_brain_measurements['white_surface_total_area_mm^2']
- 0 98553
- Name: white_surface_total_area_mm^2, dtype: int64
- >>> stats.structural_measurements[['structure_name', 'surface_area_mm^2',
- ... 'gray_matter_volume_mm^3']].head()
- structure_name surface_area_mm^2 gray_matter_volume_mm^3
- 0 caudalanteriorcingulate 1472 4258
- 1 caudalmiddlefrontal 3039 8239
- 2 cuneus 2597 6722
- 3 entorhinal 499 2379
- 4 fusiform 3079 9064
- Load Multiple Stats Files
- ~~~~~~~~~~~~~~~~~~~~~~~~~
- .. code:: python
- >>> import glob, pandas
- >>> from freesurfer_stats import CorticalParcellationStats
- >>> def load_whole_brain_measurements(stats_path) -> pandas.DataFrame:
- ... stats = CorticalParcellationStats.read(stats_path)
- ... stats.whole_brain_measurements['subject'] = stats.headers['subjectname']
- ... stats.whole_brain_measurements['source_basename'] = os.path.basename(stats_path)
- ... stats.whole_brain_measurements['hemisphere'] = stats.hemisphere
- ... return stats.whole_brain_measurements
- ...
- >>> whole_brain_measurements = pandas.concat(
- ... map(load_whole_brain_measurements, glob.glob('tests/subjects/fabian/stats/*h.aparc*.stats')),
- ... sort=False)
- >>> whole_brain_measurements.reset_index(drop=True, inplace=True)
- >>> whole_brain_measurements[['subject', 'source_basename', 'hemisphere',
- ... 'white_surface_total_area_mm^2', 'pial_surface_total_area_mm^2']]
- subject source_basename hemisphere white_surface_total_area_mm^2 pial_surface_total_area_mm^2
- 0 fabian lh.aparc.DKTatlas.stats left 98553.0 NaN
- 1 fabian rh.aparc.stats right 99468.9 NaN
- 2 fabian rh.aparc.a2009s.stats right 99494.9 NaN
- 3 fabian rh.aparc.DKTatlas.stats right 99494.9 NaN
- 4 fabian lh.aparc.stats left 98536.5 NaN
- 5 fabian lh.aparc.pial.stats left NaN 118601.0
- 6 fabian rh.aparc.pial.stats right NaN 121260.0
- 7 fabian lh.aparc.a2009s.stats left 98553.0 NaN
- >>>
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