Exemple #1
0
    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
Exemple #3
0
    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)
Exemple #4
0
def setup():
    print 'test setup'
    if no_fsl():
        raise nose.SkipTest