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