def skullstrip_ants(name='ANTsBrainExtraction', settings=None):
from niworkflows.data import get_ants_oasis_template_ras
if settings is None:
settings = {'debug': False}
workflow = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(fields=['in_file', 'source_file']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['out_file', 'out_mask', 'out_report']), name='outputnode')
t1_skull_strip = pe.Node(BrainExtractionRPT(
dimension=3, use_floatingpoint_precision=1,
debug=settings['debug'], generate_report=True,
num_threads=settings['ants_nthreads']),
name='Ants_T1_Brain_Extraction')
# should not be necesssary byt does not hurt - make sure the multiproc
# scheduler knows the resource limits
t1_skull_strip.interface.num_threads = settings['ants_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'),
('out_report', 'out_report')])
])
return workflow
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 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
def init_skullstrip_ants_wf(skull_strip_template, 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(skull_strip_template='OASIS', debug=False, omp_nthreads=1)
**Parameters**
skull_strip_template : str
Name of ANTs skull-stripping template ('OASIS' or 'NKI')
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
"""
if skull_strip_template == 'OASIS':
from niworkflows.data import get_ants_oasis_template_ras
template_dir = get_ants_oasis_template_ras()
brain_template = op.join(template_dir, 'T_template0.nii.gz')
brain_probability_mask = op.join(
template_dir, 'T_template0_BrainCerebellumProbabilityMask.nii.gz')
extraction_registration_mask = op.join(
template_dir, 'T_template0_BrainCerebellumRegistrationMask.nii.gz')
elif skull_strip_template == 'NKI':
from niworkflows.data.getters import get_ants_nki_template_ras
template_dir = get_ants_nki_template_ras()
brain_template = op.join(template_dir, 'T_template.nii.gz')
brain_probability_mask = op.join(
template_dir, 'T_template_BrainCerebellumProbabilityMask.nii.gz')
extraction_registration_mask = op.join(
template_dir, 'T_template_BrainCerebellumExtractionMask.nii.gz')
else:
raise ValueError("Unknown skull-stripping template; select from {OASIS, NKI}")
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_segs', 'out_report']),
name='outputnode')
t1_skull_strip = pe.Node(
BrainExtraction(dimension=3, use_floatingpoint_precision=1, debug=debug,
keep_temporary_files=1),
name='t1_skull_strip', n_procs=omp_nthreads)
t1_skull_strip.inputs.brain_template = brain_template
t1_skull_strip.inputs.brain_probability_mask = brain_probability_mask
t1_skull_strip.inputs.extraction_registration_mask = extraction_registration_mask
workflow.connect([
(inputnode, t1_skull_strip, [('in_file', 'anatomical_image')]),
(t1_skull_strip, outputnode, [('BrainExtractionMask', 'out_mask'),
('BrainExtractionBrain', 'out_file'),
('BrainExtractionSegmentation', 'out_segs'),
('N4Corrected0', 'bias_corrected')])
])
return workflow
