def test_execution_processing(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_dwi = os.path.join(get_home(), 'processing', 'dwi_crop.nii.gz')
in_bias = os.path.join(get_home(), 'processing', 'bias_field_b0.nii.gz')
ret = script_runner.run('scil_apply_bias_field_on_dwi.py', in_dwi, in_bias,
'dwi_crop_n4.nii.gz')
assert ret.success
def test_execution_tractometry(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_mask = os.path.join(get_home(), 'tractometry', 'IFGWM.nii.gz')
in_ref = os.path.join(get_home(), 'tractometry', 'mni_masked.nii.gz')
ret = script_runner.run('scil_compute_metrics_stats_in_ROI.py', in_mask,
'--metrics', in_ref)
assert ret.success
def test_execution_processing(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_x = os.path.join(get_home(), 'plot', 'fa.nii.gz')
in_y = os.path.join(get_home(), 'plot', 'ad.nii.gz')
ret = script_runner.run('scil_visualize_scatterplot.py', in_x, in_y,
'scatter_plot.png')
assert ret.success
def test_execution_tractometry(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_bundle = os.path.join(get_home(), 'tractometry', 'IFGWM.trk')
in_ref = os.path.join(get_home(), 'tractometry', 'mni_masked.nii.gz')
ret = script_runner.run('scil_compute_bundle_mean_std.py', in_bundle,
in_ref, '--density_weighting', '--include_dps')
assert ret.success
def test_execution_surface_vtk_fib(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_surf = os.path.join(get_home(), 'surface_vtk_fib', 'lhpialt.vtk')
in_aff = os.path.join(get_home(), 'surface_vtk_fib', 'affine.txt')
ret = script_runner.run('scil_apply_transform_to_surface.py', in_surf,
in_aff, 'lhpialt_lin.vtk')
assert ret.success
def test_execution_tractometry(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_bundle = os.path.join(get_home(), 'tractometry', 'IFGWM.trk')
in_centroid = os.path.join(get_home(), 'tractometry', 'IFGWM_uni_c_10.trk')
ret = script_runner.run('scil_bundle_voxel_label_map.py', in_bundle,
in_centroid, 'IFGWM_labels_map.nii.gz')
assert ret.success
def test_execution_4D(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_img = os.path.join(get_home(), 'commit_amico', 'dwi.nii.gz')
in_ref = os.path.join(get_home(), 'others', 't1.nii.gz')
ret = script_runner.run('scil_reshape_to_reference.py', in_img, in_ref,
'dwi_reshape.nii.gz', '--interpolation', 'nearest')
assert ret.success
def test_roi_radii_shape_parameter(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_dwi = os.path.join(get_home(), 'commit_amico',
'dwi.nii.gz')
in_bval = os.path.join(get_home(), 'commit_amico',
'dwi.bval')
in_bvec = os.path.join(get_home(), 'commit_amico',
'dwi.bvec')
mask = os.path.join(get_home(), 'commit_amico',
'mask.nii.gz')
ret = script_runner.run('scil_compute_msmt_frf.py', in_dwi,
in_bval, in_bvec, 'wm_frf.txt', 'gm_frf.txt',
'csf_frf.txt', '--mask', mask, '--roi_radii',
'37', '-f')
assert ret.success
ret = script_runner.run('scil_compute_msmt_frf.py', in_dwi,
in_bval, in_bvec, 'wm_frf.txt', 'gm_frf.txt',
'csf_frf.txt', '--mask', mask, '--roi_radii',
'37', '37', '37', '-f')
assert ret.success
ret = script_runner.run('scil_compute_msmt_frf.py', in_dwi,
in_bval, in_bvec, 'wm_frf.txt', 'gm_frf.txt',
'csf_frf.txt', '--mask', mask, '--roi_radii',
'37', '37', '37', '37', '37', '-f')
assert (not ret.success)
def test_execution_connectivity_div(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_sc = os.path.join(get_home(), 'connectivity', 'sc.npy')
in_vol = os.path.join(get_home(), 'connectivity', 'vol.npy')
ret = script_runner.run('scil_connectivity_math.py', 'division', in_sc,
in_vol, 'sc_norm_vol.npy')
assert ret.success
def test_execution_surface_vtk_fib(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_fib = os.path.join(get_home(), 'surface_vtk_fib', 'gyri_fanning.fib')
in_fa = os.path.join(get_home(), 'surface_vtk_fib', 'fa.nii.gz')
ret = script_runner.run('scil_convert_tractogram.py', in_fib,
'gyri_fanning.trk', '--reference', in_fa)
assert ret.success
def test_execution_processing(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_fa = os.path.join(get_home(), 'processing', 'fa.nii.gz')
in_mask = os.path.join(get_home(), 'processing', 'seed.nii.gz')
ret = script_runner.run('scil_visualize_histogram.py', in_fa, in_mask,
'20', 'histogram.png')
assert ret.success
def test_execution_processing(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_dwi = os.path.join(get_home(), 'processing', 'dwi_crop.nii.gz')
in_bval = os.path.join(get_home(), 'processing', 'dwi.bval')
in_bvec = os.path.join(get_home(), 'processing', 'dwi.bvec')
ret = script_runner.run('scil_extract_b0.py', in_dwi, in_bval, in_bvec,
'b0_mean.nii.gz', '--mean', '--b0', '20')
assert ret.success
def test_score_bundles(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_tractogram = os.path.join(get_home(), 'tracking', 'pft.trk')
models = os.path.join(get_home(), 'tracking', 'seeding_mask.nii.gz')
endpoints = os.path.join(get_home(), 'tracking', 'interface.nii.gz')
ret = script_runner.run('scil_score_tractogram.py', in_tractogram, models,
'--gt_endpoints', endpoints)
assert ret.success
def test_execution_add(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_img_1 = os.path.join(get_home(), 'atlas', 'brainstem_173.nii.gz')
in_img_2 = os.path.join(get_home(), 'atlas', 'brainstem_174.nii.gz')
in_img_3 = os.path.join(get_home(), 'atlas', 'brainstem_175.nii.gz')
ret = script_runner.run('scil_image_math.py', 'addition', in_img_1,
in_img_2, in_img_3, 'brainstem.nii.gz')
assert ret.success
def test_execution_processing(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_dwi = os.path.join(get_home(), 'processing', 'dwi_crop.nii.gz')
in_bval = os.path.join(get_home(), 'processing', 'dwi.bval')
in_bvec = os.path.join(get_home(), 'processing', 'dwi.bvec')
ret = script_runner.run('scil_compute_ssst_frf.py', in_dwi, in_bval,
in_bvec, 'frf.txt', '-f')
assert ret.success
def test_execution_connectivity(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_sc = os.path.join(get_home(), 'connectivity', 'sc_norm.npy')
in_len = os.path.join(get_home(), 'connectivity', 'len.npy')
ret = script_runner.run('scil_evaluate_connectivity_measures.py', in_sc,
in_len, 'gtm.json', '--avg_node_wise',
'--small_world')
assert ret.success
def test_execution_processing(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_dwi = os.path.join(get_home(), 'processing', 'dwi_crop.nii.gz')
in_bval = os.path.join(get_home(), 'processing', 'dwi.bval')
in_bvec = os.path.join(get_home(), 'processing', 'dwi.bvec')
ret = script_runner.run('scil_split_image.py', in_dwi, in_bval, in_bvec,
'dwi', '5', '15', '25')
assert ret.success
def test_execution_connectivity(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_sc = os.path.join(get_home(), 'connectivity', 'sc_norm.npy')
in_len = os.path.join(get_home(), 'connectivity', 'len.npy')
ret = script_runner.run(
'scil_evaluate_connectivity_pairwise_agreement_measures.py', in_sc,
in_len, 'diff.json', '--single_compare', in_sc)
assert ret.success
def test_execution_processing(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_dwi = os.path.join(get_home(), 'processing', 'dwi_crop_3000.nii.gz')
in_bval = os.path.join(get_home(), 'processing', '3000.bval')
in_bvec = os.path.join(get_home(), 'processing', '3000.bvec')
ret = script_runner.run('scil_compute_sh_from_signal.py', in_dwi, in_bval,
in_bvec, 'sh_1000.nii.gz')
assert ret.success
def test_execution_filtering(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_tractogram = os.path.join(get_home(), 'filtering', 'bundle_all_1mm.trk')
in_mask = os.path.join(get_home(), 'filtering', 'mask.nii.gz')
ret = script_runner.run('scil_cut_streamlines.py', in_tractogram, in_mask,
'out_tractogram_cut.trk', '--resample', '0.2',
'--compress', '0.1')
assert ret.success
def test_execution_tractometry(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_bundle = os.path.join(get_home(), 'tractometry', 'IFGWM_uni.trk')
in_ref = os.path.join(get_home(), 'tractometry', 'mni_masked.nii.gz')
ret = script_runner.run('scil_endpoints_metric.py', in_bundle, in_ref,
'out/')
assert ret.success
def test_execution_connectivity(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_sc = os.path.join(get_home(), 'connectivity', 'sc.npy')
in_sim = os.path.join(get_home(), 'connectivity', 'len.npy')
ret = script_runner.run('scil_filter_connectivity.py', 'mask.npy',
'--greater_than', in_sc, '5', '1',
'--greater_than', in_sim, '0', '1',
'--keep_condition_count')
assert ret.success
def test_execution_tractometry(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_bundle = os.path.join(get_home(), 'tractometry', 'IFGWM.trk')
in_labels = os.path.join(get_home(), 'tractometry',
'IFGWM_labels_map.nii.gz')
ret = script_runner.run('scil_estimate_bundles_diameter.py', in_bundle,
in_labels, '--wireframe', '--fitting_func',
'lin_up')
assert ret.success
def test_execution_connectivity(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_h5 = os.path.join(get_home(), 'connectivity', 'decompose.h5')
in_fodf = os.path.join(get_home(), 'connectivity', 'fodf.nii.gz')
ret = script_runner.run('scil_compute_mean_fixel_afd_from_hdf5.py', in_h5,
in_fodf, 'decompose_afd.nii.gz',
'--length_weighting', '--sh_basis', 'descoteaux07',
'--processes', '1')
assert ret.success
def test_execution_tracking(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_wm = os.path.join(get_home(), 'tracking', 'map_wm.nii.gz')
in_gm = os.path.join(get_home(), 'tracking', 'map_gm.nii.gz')
in_csf = os.path.join(get_home(), 'tracking', 'map_csf.nii.gz')
ret = script_runner.run(
'scil_compute_maps_for_particle_filter_tracking.py', in_wm, in_gm,
in_csf)
assert ret.success
def test_execution_connectivity(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_1 = os.path.join(get_home(), 'connectivity', 'sc.npy')
in_2 = os.path.join(get_home(), 'connectivity', 'sc_norm.npy')
in_mask = os.path.join(get_home(), 'connectivity', 'mask.npy')
ret = script_runner.run('scil_compare_connectivity.py', 'pval.npy',
'--in_g1', in_1, '--in_g2', in_2,
'--filtering_mask', in_mask)
assert ret.success
def test_execution_filtering(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_1 = os.path.join(get_home(), 'filtering', 'bundle_4.trk')
in_2 = os.path.join(get_home(), 'filtering', 'bundle_4_filtered.trk')
in_3 = os.path.join(get_home(), 'filtering',
'bundle_4_filtered_no_loops.trk')
ret = script_runner.run('scil_perform_majority_vote.py', in_1, in_2, in_3,
'--ratio_streamlines', '0.5', '--same_tractogram')
assert ret.success
def test_execution_processing(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_tracking = os.path.join(get_home(), 'processing', 'tracking.trk')
in_fodf = os.path.join(get_home(), 'processing',
'fodf_descoteaux07.nii.gz')
ret = script_runner.run('scil_compute_mean_fixel_afd_from_bundles.py',
in_tracking, in_fodf, 'afd_test.nii.gz',
'--sh_basis', 'descoteaux07', '--length_weighting')
assert ret.success
def test_execution_processing_3000(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_dwi = os.path.join(get_home(), 'processing', 'dwi_crop.nii.gz')
in_bval = os.path.join(get_home(), 'processing', 'dwi.bval')
in_bvec = os.path.join(get_home(), 'processing', 'dwi.bvec')
ret = script_runner.run('scil_extract_dwi_shell.py', in_dwi, in_bval,
in_bvec, '0', '3000', 'dwi_crop_3000.nii.gz',
'3000.bval', '3000.bvec', '-t', '30')
assert ret.success
def test_execution_connectivity(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_h5 = os.path.join(get_home(), 'connectivity', 'decompose.h5')
in_target = os.path.join(get_home(), 'connectivity',
'endpoints_atlas.nii.gz')
in_transfo = os.path.join(get_home(), 'connectivity', 'affine.txt')
ret = script_runner.run('scil_apply_transform_to_hdf5.py', in_h5,
in_target, in_transfo, 'decompose_lin.h5')
assert ret.success