pipeline.connect(tbss, 'tbss4.outputnode.projectedfa_file', tbss4_test_all_FA_skeletonised, 'volume1') pipeline.connect(tbss4_original_datasource, 'all_FA_skeletonised', tbss4_test_all_FA_skeletonised, 'volume2') pipeline.connect(tbss, 'tbss4.outputnode.skeleton_mask', tbss4_test_mean_FA_skeleton_mask, 'volume1') pipeline.connect(tbss4_original_datasource, 'mean_FA_skeleton_mask', tbss4_test_mean_FA_skeleton_mask, 'volume2') pipeline.run(plugin='Linear') os.chdir(old_dir) shutil.rmtree(test_dir) # this test is disabled until we figure out what is wrong with TBSS in 5.0.9 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed") @pytest.mark.skipif(no_fsl_course_data(), reason="fsl data not available") def test_disabled_tbss_est_skeleton(): _tbss_test_helper(True) # this test is disabled until we figure out what is wrong with TBSS in 5.0.9 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed") @pytest.mark.skipif(no_fsl_course_data(), reason="fsl data not available") def test_disabled_tbss_est_skeleton_use_precomputed_skeleton(): _tbss_test_helper(False)
Reorient2Std, RobustFOV, ) from nipype.interfaces.fsl.base import no_fsl from nipype.interfaces.mrtrix3 import ( ConstrainedSphericalDeconvolution, DWIBiasCorrect, DWIDenoise, Generate5tt, MRDeGibbs, ResponseSD, ) #: Warn if FSL is not accessible. test_mode = getattr(settings, "TESTING_MODE", False) if no_fsl() and not test_mode: warnings.warn(messages.NO_FSL) _NIPYPE_VERSION = nipype.__version__ #: Preconfigured analysis definitions. analysis_definitions = [ { "title": "BET", "description": "FSL brain extraction (BET).", "versions": [{ "title": BET().version or "1.0", "description": f"Default BET version for nipype {_NIPYPE_VERSION}.", # noqa: E501
tbss4_original_datasource.inputs.template = 'stats/%s.nii.gz' tbss4_original_datasource.inputs.template_args = dict(all_FA_skeletonised=[['all_FA_skeletonised']], mean_FA_skeleton_mask=[['mean_FA_skeleton_mask']]) tbss4_test_all_FA_skeletonised = pe.Node(util.AssertEqual(), name="tbss4_test_all_FA_skeletonised") tbss4_test_mean_FA_skeleton_mask = pe.Node(util.AssertEqual(), name="tbss4_test_mean_FA_skeleton_mask") pipeline.connect(tbss, 'tbss4.outputnode.projectedfa_file', tbss4_test_all_FA_skeletonised, 'volume1') pipeline.connect(tbss4_original_datasource, 'all_FA_skeletonised', tbss4_test_all_FA_skeletonised, 'volume2') pipeline.connect(tbss, 'tbss4.outputnode.skeleton_mask', tbss4_test_mean_FA_skeleton_mask, 'volume1') pipeline.connect(tbss4_original_datasource, 'mean_FA_skeleton_mask', tbss4_test_mean_FA_skeleton_mask, 'volume2') pipeline.run(plugin='Linear') os.chdir(old_dir) shutil.rmtree(test_dir) # this test is disabled until we figure out what is wrong with TBSS in 5.0.9 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed") @pytest.mark.skipif(no_fsl_course_data(), reason="fsl data not available") def disabled_tbss_est_skeleton(): _tbss_test_helper(True) # this test is disabled until we figure out what is wrong with TBSS in 5.0.9 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed") @pytest.mark.skipif(no_fsl_course_data(), reason="fsl data not available") def disabled_tbss_est_skeleton_use_precomputed_skeleton(): _tbss_test_helper(False)
def setup(): print 'test setup' if no_fsl(): raise nose.SkipTest