freesurfer-stats ================ .. image:: https://img.shields.io/badge/code%20style-black-000000.svg :target: https://github.com/psf/black .. 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/ .. image:: https://zenodo.org/badge/194054168.svg :target: https://zenodo.org/badge/latestdoi/194054168 Python Library to Read FreeSurfer's Cortical Parcellation Anatomical Statistics `subject/stats/[rl]h.aparc.*.stats` 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['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 Load Stats File From Webserver, Amazon S3 or Google Cloud Storage ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. code:: python >>> from freesurfer_stats import CorticalParcellationStats >>> stats = CorticalParcellationStats.read('https://[...]/stats/rh.aparc.stats') >>> stats.whole_brain_measurements['total_cortical_gray_matter_volume_mm^3'] 0 553998.311189 Name: total_cortical_gray_matter_volume_mm^3, dtype: float64 Replace ``https://`` with ``s3://`` or ``gcs://``. Credentials for S3 may be provided in ``~/.aws/credentials`` or via environment variables. See `S3Fs docs `__. Tests ----- .. code:: sh pip3 install --user pipenv git clone https://github.com/fphammerle/freesurfer-stats.git cd freesurfer-stats pipenv sync --dev pipenv run pylint freesurfer_stats pipenv run pytest