def test_BrainExtractionRPT(monkeypatch, oasis_dir, moving, nthreads):
""" test antsBrainExtraction with reports"""
def _agg(objekt, runtime):
outputs = Bunch(BrainExtractionMask=os.path.join(
datadir, 'testBrainExtractionRPTBrainExtractionMask.nii.gz')
)
return outputs
# Patch the _run_interface method
monkeypatch.setattr(BrainExtractionRPT, '_run_interface',
_run_interface_mock)
monkeypatch.setattr(BrainExtractionRPT, 'aggregate_outputs',
_agg)
bex_rpt = BrainExtractionRPT(
generate_report=True,
dimension=3,
use_floatingpoint_precision=1,
anatomical_image=moving,
brain_template=os.path.join(oasis_dir, 'T_template0.nii.gz'),
brain_probability_mask=os.path.join(
oasis_dir, 'T_template0_BrainCerebellumProbabilityMask.nii.gz'),
extraction_registration_mask=os.path.join(
oasis_dir, 'T_template0_BrainCerebellumRegistrationMask.nii.gz'),
out_prefix='testBrainExtractionRPT',
debug=True, # run faster for testing purposes
num_threads=nthreads
)
_smoke_test_report(bex_rpt, 'testANTSBrainExtraction.svg')
def init_skullstrip_ants_wf(debug, omp_nthreads, name='skullstrip_ants_wf'):
from niworkflows.data import get_ants_oasis_template_ras
workflow = pe.Workflow(name=name)
inputnode = pe.Node(
niu.IdentityInterface(fields=['in_file', 'source_file']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['bias_corrected', 'out_file', 'out_mask', 'out_report']),
name='outputnode')
t1_skull_strip = pe.Node(BrainExtractionRPT(dimension=3,
use_floatingpoint_precision=1,
debug=debug,
generate_report=True,
num_threads=omp_nthreads,
keep_temporary_files=1),
name='t1_skull_strip')
# should not be necesssary byt does not hurt - make sure the multiproc
# scheduler knows the resource limits
t1_skull_strip.interface.num_threads = omp_nthreads
t1_skull_strip.inputs.brain_template = op.join(
get_ants_oasis_template_ras(), 'T_template0.nii.gz')
t1_skull_strip.inputs.brain_probability_mask = op.join(
get_ants_oasis_template_ras(),
'T_template0_BrainCerebellumProbabilityMask.nii.gz')
t1_skull_strip.inputs.extraction_registration_mask = op.join(
get_ants_oasis_template_ras(),
'T_template0_BrainCerebellumRegistrationMask.nii.gz')
workflow.connect([
(inputnode, t1_skull_strip, [('in_file', 'anatomical_image')]),
(t1_skull_strip, outputnode, [('BrainExtractionMask', 'out_mask'),
('BrainExtractionBrain', 'out_file'),
('N4Corrected0', 'bias_corrected'),
('out_report', 'out_report')])
])
return workflow
def test_BrainExtractionRPT(monkeypatch, moving, nthreads):
""" test antsBrainExtraction with reports"""
def _agg(objekt, runtime):
outputs = objekt.output_spec()
outputs.BrainExtractionMask = os.path.join(
datadir, "testBrainExtractionRPTBrainExtractionMask.nii.gz")
outputs.out_report = os.path.join(runtime.cwd,
objekt.inputs.out_report)
return outputs
# Patch the _run_interface method
monkeypatch.setattr(BrainExtractionRPT, "_run_interface",
_run_interface_mock)
monkeypatch.setattr(BrainExtractionRPT, "aggregate_outputs", _agg)
bex_rpt = BrainExtractionRPT(
generate_report=True,
dimension=3,
use_floatingpoint_precision=1,
anatomical_image=moving,
brain_template=str(
get_template("OASIS30ANTs", resolution=1, desc=None,
suffix="T1w")),
brain_probability_mask=str(
get_template("OASIS30ANTs",
resolution=1,
label="brain",
suffix="probseg")),
extraction_registration_mask=str(
get_template(
"OASIS30ANTs",
resolution=1,
desc="BrainCerebellumRegistration",
suffix="mask",
)),
out_prefix="testBrainExtractionRPT",
debug=True, # run faster for testing purposes
num_threads=nthreads,
)
_smoke_test_report(bex_rpt, "testANTSBrainExtraction.svg")
def test_generate_report(self):
''' test of BrainExtractionRPT under basic conditions:
- dimension=3
- use_floatingpoint_precision=1,
- brain_template, brain_probability_mask, extraction_registration_mask from get_ants_oasis_template_ras()
'''
_smoke_test_report(
BrainExtractionRPT(
generate_report=True,
dimension=3,
use_floatingpoint_precision=1,
anatomical_image=MNI_2MM,
brain_template=_template_name('T_template0.nii.gz'),
brain_probability_mask=_template_name(
'T_template0_BrainCerebellumProbabilityMask.nii.gz'),
extraction_registration_mask=_template_name(
'T_template0_BrainCerebellumRegistrationMask.nii.gz'),
out_prefix='testBrainExtractionRPT',
debug=True, # run faster for testing purposes
num_threads=cpu_count()),
'testANTSBrainExtraction.html')
def init_skullstrip_ants_wf(debug, omp_nthreads, name='skullstrip_ants_wf'):
r"""
This workflow performs skull-stripping using ANTs' ``BrainExtraction.sh``
.. workflow::
:graph2use: orig
:simple_form: yes
from fmriprep.workflows.anatomical import init_skullstrip_ants_wf
wf = init_skullstrip_ants_wf(debug=False, omp_nthreads=1)
**Parameters**
debug : bool
Enable debugging outputs
omp_nthreads : int
Maximum number of threads an individual process may use
**Inputs**
in_file
T1-weighted structural image to skull-strip
**Outputs**
bias_corrected
Bias-corrected ``in_file``, before skull-stripping
out_file
Skull-stripped ``in_file``
out_mask
Binary mask of the skull-stripped ``in_file``
out_report
Reportlet visualizing quality of skull-stripping
"""
from niworkflows.data import get_ants_oasis_template_ras
workflow = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(fields=['in_file']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['bias_corrected', 'out_file', 'out_mask', 'out_report']),
name='outputnode')
t1_skull_strip = pe.Node(BrainExtractionRPT(dimension=3,
use_floatingpoint_precision=1,
debug=debug,
generate_report=True,
num_threads=omp_nthreads,
keep_temporary_files=1),
name='t1_skull_strip',
n_procs=omp_nthreads)
t1_skull_strip.inputs.brain_template = op.join(
get_ants_oasis_template_ras(), 'T_template0.nii.gz')
t1_skull_strip.inputs.brain_probability_mask = op.join(
get_ants_oasis_template_ras(),
'T_template0_BrainCerebellumProbabilityMask.nii.gz')
t1_skull_strip.inputs.extraction_registration_mask = op.join(
get_ants_oasis_template_ras(),
'T_template0_BrainCerebellumRegistrationMask.nii.gz')
workflow.connect([
(inputnode, t1_skull_strip, [('in_file', 'anatomical_image')]),
(t1_skull_strip, outputnode, [('BrainExtractionMask', 'out_mask'),
('BrainExtractionBrain', 'out_file'),
('N4Corrected0', 'bias_corrected'),
('out_report', 'out_report')])
])
return workflow