"""
5. Template is initialized by a simple average in this simple example,
any reference image could be used (i.e. a previously created template)
"""
initAvg = pe.Node(interface=ants.AverageImages(), name ='initAvg')
initAvg.inputs.dimension = 3
initAvg.inputs.normalize = True
tbuilder.connect(datasource, "InitialTemplateInputs", initAvg, "images")
"""
6. Define the first iteration of template building
"""
buildTemplateIteration1=antsRegistrationTemplateBuildSingleIterationWF('iteration01')
"""
Here we are fine tuning parameters of the SGE job (memory limit, numebr of cores etc.)
"""
BeginANTS = buildTemplateIteration1.get_node("BeginANTS")
BeginANTS.plugin_args={'qsub_args': '-S /bin/bash -pe smp1 8-12 -l mem_free=6000M -o /dev/null -e /dev/null queue_name', 'overwrite': True}
tbuilder.connect(initAvg, 'output_average_image', buildTemplateIteration1, 'inputspec.fixed_image')
tbuilder.connect(datasource, 'ListOfImagesDictionaries', buildTemplateIteration1, 'inputspec.ListOfImagesDictionaries')
tbuilder.connect(datasource, 'registrationImageTypes', buildTemplateIteration1, 'inputspec.registrationImageTypes')
tbuilder.connect(datasource, 'interpolationMapping', buildTemplateIteration1, 'inputspec.interpolationMapping')
"""
7. Define the second iteration of template building
datasource.inputs.interpolationMapping = interpolationMapping
"""
5. Template is initialized by a simple average in this simple example,
any reference image could be used (i.e. a previously created template)
"""
initAvg = pe.Node(interface=ants.AverageImages(), name='initAvg')
initAvg.inputs.dimension = 3
initAvg.inputs.normalize = True
tbuilder.connect(datasource, "InitialTemplateInputs", initAvg, "images")
"""
6. Define the first iteration of template building
"""
buildTemplateIteration1 = antsRegistrationTemplateBuildSingleIterationWF(
'iteration01')
"""
Here we are fine tuning parameters of the SGE job (memory limit, numebr of cores etc.)
"""
BeginANTS = buildTemplateIteration1.get_node("BeginANTS")
BeginANTS.plugin_args = {
'qsub_args':
'-S /bin/bash -pe smp1 8-12 -l mem_free=6000M -o /dev/null -e /dev/null queue_name',
'overwrite': True
}
tbuilder.connect(initAvg, 'output_average_image', buildTemplateIteration1,
'inputspec.fixed_image')
tbuilder.connect(datasource, 'ListOfImagesDictionaries',
buildTemplateIteration1, 'inputspec.ListOfImagesDictionaries')
"""
5. Template is initialized by a simple average in this simple example,
any reference image could be used (i.e. a previously created template)
"""
initAvg = pe.Node(interface=ants.AverageImages(), name="initAvg")
initAvg.inputs.dimension = 3
initAvg.inputs.normalize = True
tbuilder.connect(datasource, "InitialTemplateInputs", initAvg, "images")
"""
6. Define the first iteration of template building
"""
buildTemplateIteration1 = antsRegistrationTemplateBuildSingleIterationWF("iteration01")
"""
Here we are fine tuning parameters of the SGE job (memory limit, numebr of cores etc.)
"""
BeginANTS = buildTemplateIteration1.get_node("BeginANTS")
BeginANTS.plugin_args = {
"qsub_args": "-S /bin/bash -pe smp1 8-12 -l mem_free=6000M -o /dev/null -e /dev/null queue_name",
"overwrite": True,
}
tbuilder.connect(initAvg, "output_average_image", buildTemplateIteration1, "inputspec.fixed_image")
tbuilder.connect(datasource, "ListOfImagesDictionaries", buildTemplateIteration1, "inputspec.ListOfImagesDictionaries")
tbuilder.connect(datasource, "registrationImageTypes", buildTemplateIteration1, "inputspec.registrationImageTypes")
tbuilder.connect(datasource, "interpolationMapping", buildTemplateIteration1, "inputspec.interpolationMapping")