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- import datetime
- import os
- import pandas.util.testing
- import pytest
- from conftest import SUBJECTS_DIR, assert_approx_equal
- from freesurfer_stats import CorticalParcellationStats
- @pytest.mark.parametrize(
- ('path', 'headers', 'hemisphere',
- 'whole_brain_measurements', 'structure_measurements'),
- [(os.path.join(SUBJECTS_DIR, 'fabian', 'stats', 'lh.aparc.DKTatlas.stats.short'),
- {'CreationTime': datetime.datetime(2019, 5, 9, 21, 5, 54, tzinfo=datetime.timezone.utc),
- 'generating_program': 'mris_anatomical_stats',
- 'cvs_version': 'Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp',
- 'mrisurf.c-cvs_version': 'Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp',
- 'cmdline': 'mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label'
- ' -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot'
- ' -c ../label/aparc.annot.DKTatlas.ctab fabian lh white',
- 'sysname': 'Linux',
- 'hostname': 'another-hostname',
- 'machine': 'x86_64',
- 'user': 'some-username',
- 'SUBJECTS_DIR': '/home/some-username/freesurfer-subjects',
- 'anatomy_type': 'surface',
- 'subjectname': 'fabian',
- 'hemi': 'lh',
- 'AnnotationFile': '../label/lh.aparc.DKTatlas.annot',
- 'AnnotationFileTimeStamp': datetime.datetime(2019, 5, 9, 23, 5, 40)},
- 'left',
- {'White Surface Total Area': (98553, 'mm^2'),
- 'Mean Thickness': (2.50462, 'mm'),
- 'Brain Segmentation Volume': (1327432.000000, 'mm^3'),
- 'Brain Segmentation Volume Without Ventricles': (1316285.000000, 'mm^3'),
- 'Brain Segmentation Volume Without Ventricles from Surf': (1315572.548920, 'mm^3'),
- 'Total cortical gray matter volume': (553998.311189, 'mm^3'),
- 'Supratentorial volume': (1172669.548920, 'mm^3'),
- 'Supratentorial volume Without Ventricles': (1164180.548920, 'mm^3'),
- 'Estimated Total Intracranial Volume': (1670487.274486, 'mm^3')},
- [{'Structure Name': 'caudalanteriorcingulate',
- 'Number of Vertices': 2061,
- 'Surface Area (mm^2)': 1472,
- 'Gray Matter Volume (mm^3)': 4258,
- 'Average Thickness (mm)': 2.653,
- 'Thickness StdDev (mm)': 0.644,
- 'Integrated Rectified Mean Curvature (mm^-1)': 0.135,
- 'Integrated Rectified Gaussian Curvature (mm^-2)': 0.020,
- 'Folding Index': 27,
- 'Intrinsic Curvature Index': 1.6},
- {'Structure Name': 'caudalmiddlefrontal',
- 'Number of Vertices': 4451,
- 'Surface Area (mm^2)': 3039,
- 'Gray Matter Volume (mm^3)': 8239,
- 'Average Thickness (mm)': 2.456,
- 'Thickness StdDev (mm)': 0.486,
- 'Integrated Rectified Mean Curvature (mm^-1)': 0.116,
- 'Integrated Rectified Gaussian Curvature (mm^-2)': 0.020,
- 'Folding Index': 42,
- 'Intrinsic Curvature Index': 3.7},
- {'Structure Name': 'insula',
- 'Number of Vertices': 3439,
- 'Surface Area (mm^2)': 2304,
- 'Gray Matter Volume (mm^3)': 7594,
- 'Average Thickness (mm)': 3.193,
- 'Thickness StdDev (mm)': 0.620,
- 'Integrated Rectified Mean Curvature (mm^-1)': 0.116,
- 'Integrated Rectified Gaussian Curvature (mm^-2)': 0.027,
- 'Folding Index': 33,
- 'Intrinsic Curvature Index': 3.5}]),
- (os.path.join(
- SUBJECTS_DIR, 'fabian', 'stats', 'rh.aparc.pial.stats.short'),
- {'CreationTime': datetime.datetime(2019, 5, 9, 21, 3, 42, tzinfo=datetime.timezone.utc),
- 'generating_program': 'mris_anatomical_stats',
- 'cvs_version': 'Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp',
- 'mrisurf.c-cvs_version': 'Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp',
- 'cmdline': 'mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label'
- ' -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot'
- ' -c ../label/aparc.annot.ctab fabian rh pial',
- 'sysname': 'Linux',
- 'hostname': 'some-hostname',
- 'machine': 'x86_64',
- 'user': 'some-username',
- 'SUBJECTS_DIR': '/home/some-username/freesurfer-subjects',
- 'anatomy_type': 'surface',
- 'subjectname': 'fabian',
- 'hemi': 'rh',
- 'AnnotationFile': '../label/rh.aparc.annot',
- 'AnnotationFileTimeStamp': datetime.datetime(2019, 5, 9, 22, 27, 28)},
- 'right',
- {'Pial Surface Total Area': (121260, 'mm^2'),
- 'Mean Thickness': (2.4817, 'mm'),
- 'Brain Segmentation Volume': (1327432.000000, 'mm^3'),
- 'Brain Segmentation Volume Without Ventricles': (1316285.000000, 'mm^3'),
- 'Brain Segmentation Volume Without Ventricles from Surf': (1315572.548920, 'mm^3'),
- 'Total cortical gray matter volume': (553998.311189, 'mm^3'),
- 'Supratentorial volume': (1172669.548920, 'mm^3'),
- 'Supratentorial volume Without Ventricles': (1164180.548920, 'mm^3'),
- 'Estimated Total Intracranial Volume': (1670487.274486, 'mm^3')},
- [{'Structure Name': 'bankssts',
- 'Number of Vertices': 1344,
- 'Surface Area (mm^2)': 825,
- 'Gray Matter Volume (mm^3)': 2171,
- 'Average Thickness (mm)': 2.436,
- 'Thickness StdDev (mm)': 0.381,
- 'Integrated Rectified Mean Curvature (mm^-1)': 0.115,
- 'Integrated Rectified Gaussian Curvature (mm^-2)': 0.028,
- 'Folding Index': 19,
- 'Intrinsic Curvature Index': 1.7},
- {'Structure Name': 'transversetemporal',
- 'Number of Vertices': 651,
- 'Surface Area (mm^2)': 545,
- 'Gray Matter Volume (mm^3)': 1061,
- 'Average Thickness (mm)': 2.251,
- 'Thickness StdDev (mm)': 0.317,
- 'Integrated Rectified Mean Curvature (mm^-1)': 0.110,
- 'Integrated Rectified Gaussian Curvature (mm^-2)': 0.021,
- 'Folding Index': 3,
- 'Intrinsic Curvature Index': 0.6}])],
- )
- def test_read(path, headers, hemisphere, whole_brain_measurements, structure_measurements):
- stats = CorticalParcellationStats.read(path)
- assert headers == stats.headers
- assert hemisphere == stats.hemisphere
- assert_approx_equal(whole_brain_measurements,
- stats.whole_brain_measurements)
- assert list(stats.structure_measurements.columns) == [
- 'Structure Name',
- 'Number of Vertices',
- 'Surface Area (mm^2)',
- 'Gray Matter Volume (mm^3)',
- 'Average Thickness (mm)',
- 'Thickness StdDev (mm)',
- 'Integrated Rectified Mean Curvature (mm^-1)',
- 'Integrated Rectified Gaussian Curvature (mm^-2)',
- 'Folding Index',
- 'Intrinsic Curvature Index',
- ]
- pandas.util.testing.assert_frame_equal(
- left=pandas.DataFrame(structure_measurements),
- right=stats.structure_measurements,
- check_like=True, # ignore the order of index & columns
- check_dtype=True,
- check_names=True,
- )
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