sMRI: Using new ANTS for creating a T1 template (ITK4)¶
In this tutorial we will use ANTS (new ITK4 version aka “antsRegistration”) based workflow to create a template out of multiple T1 volumes. We will also showcase how to fine tune SGE jobs requirements.
- Tell python where to find the appropriate functions.
import os
import nipype.interfaces.utility as util
import nipype.interfaces.ants as ants
import nipype.interfaces.io as io
import nipype.pipeline.engine as pe # pypeline engine
from nipype.workflows.smri.ants import antsRegistrationTemplateBuildSingleIterationWF
- Download T1 volumes into home directory
import urllib2
homeDir=os.getenv("HOME")
requestedPath=os.path.join(homeDir,'nipypeTestPath')
mydatadir=os.path.realpath(requestedPath)
if not os.path.exists(mydatadir):
os.makedirs(mydatadir)
print mydatadir
MyFileURLs=[
('http://slicer.kitware.com/midas3/download?bitstream=13121','01_T1_half.nii.gz'),
('http://slicer.kitware.com/midas3/download?bitstream=13122','02_T1_half.nii.gz'),
('http://slicer.kitware.com/midas3/download?bitstream=13124','03_T1_half.nii.gz'),
('http://slicer.kitware.com/midas3/download?bitstream=13128','01_T1_inv_half.nii.gz'),
('http://slicer.kitware.com/midas3/download?bitstream=13123','02_T1_inv_half.nii.gz'),
('http://slicer.kitware.com/midas3/download?bitstream=13125','03_T1_inv_half.nii.gz'),
]
for tt in MyFileURLs:
myURL=tt[0]
localFilename=os.path.join(mydatadir,tt[1])
if not os.path.exists(localFilename):
remotefile = urllib2.urlopen(myURL)
localFile = open(localFilename, 'wb')
localFile.write(remotefile.read())
localFile.close()
print("Downloaded file: {0}".format(localFilename))
else:
print("File previously downloaded {0}".format(localFilename))
ListOfImagesDictionaries - a list of dictionaries where each dictionary is for one scan session, and the mappings in the dictionary are for all the co-aligned images for that one scan session
ListOfImagesDictionaries=[
{'T1':os.path.join(mydatadir,'01_T1_half.nii.gz'),'INV_T1':os.path.join(mydatadir,'01_T1_inv_half.nii.gz'),'LABEL_MAP':os.path.join(mydatadir,'01_T1_inv_half.nii.gz')},
{'T1':os.path.join(mydatadir,'02_T1_half.nii.gz'),'INV_T1':os.path.join(mydatadir,'02_T1_inv_half.nii.gz'),'LABEL_MAP':os.path.join(mydatadir,'02_T1_inv_half.nii.gz')},
{'T1':os.path.join(mydatadir,'03_T1_half.nii.gz'),'INV_T1':os.path.join(mydatadir,'03_T1_inv_half.nii.gz'),'LABEL_MAP':os.path.join(mydatadir,'03_T1_inv_half.nii.gz')}
]
input_passive_images=[
{'INV_T1':os.path.join(mydatadir,'01_T1_inv_half.nii.gz')},
{'INV_T1':os.path.join(mydatadir,'02_T1_inv_half.nii.gz')},
{'INV_T1':os.path.join(mydatadir,'03_T1_inv_half.nii.gz')}
]
registrationImageTypes - A list of the image types to be used actively during the estimation process of registration, any image type not in this list will be passively resampled with the estimated transforms. [‘T1’,’T2’]
registrationImageTypes=['T1']
interpolationMap - A map of image types to interpolation modes. If an image type is not listed, it will be linearly interpolated. { ‘labelmap’:’NearestNeighbor’, ‘FLAIR’:’WindowedSinc’ }
interpolationMapping={'INV_T1':'LanczosWindowedSinc','LABEL_MAP':'NearestNeighbor','T1':'Linear'}
- Define the workflow and its working directory
tbuilder=pe.Workflow(name="antsRegistrationTemplateBuilder")
tbuilder.base_dir=requestedPath
- Define data sources. In real life these would be replace by DataGrabbers
InitialTemplateInputs=[ mdict['T1'] for mdict in ListOfImagesDictionaries ]
datasource = pe.Node(interface=util.IdentityInterface(fields=
['InitialTemplateInputs', 'ListOfImagesDictionaries',
'registrationImageTypes','interpolationMapping']),
run_without_submitting=True,
name='InputImages' )
datasource.inputs.InitialTemplateInputs=InitialTemplateInputs
datasource.inputs.ListOfImagesDictionaries=ListOfImagesDictionaries
datasource.inputs.registrationImageTypes=registrationImageTypes
datasource.inputs.interpolationMapping=interpolationMapping
datasource.inputs.sort_filelist = True
- 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")
- 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')
- Define the second iteration of template building
buildTemplateIteration2 = antsRegistrationTemplateBuildSingleIterationWF('iteration02')
BeginANTS = buildTemplateIteration2.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(buildTemplateIteration1, 'outputspec.template', buildTemplateIteration2, 'inputspec.fixed_image')
tbuilder.connect(datasource, 'ListOfImagesDictionaries', buildTemplateIteration2, 'inputspec.ListOfImagesDictionaries')
tbuilder.connect(datasource, 'registrationImageTypes', buildTemplateIteration2, 'inputspec.registrationImageTypes')
tbuilder.connect(datasource, 'interpolationMapping', buildTemplateIteration2, 'inputspec.interpolationMapping')
- Move selected files to a designated results folder
datasink = pe.Node(io.DataSink(), name="datasink")
datasink.inputs.base_directory = os.path.join(requestedPath, "results")
tbuilder.connect(buildTemplateIteration2, 'outputspec.template',datasink,'PrimaryTemplate')
tbuilder.connect(buildTemplateIteration2, 'outputspec.passive_deformed_templates',datasink,'PassiveTemplate')
tbuilder.connect(initAvg, 'output_average_image', datasink,'PreRegisterAverage')
- Run the workflow
tbuilder.run(plugin="SGE")
Example source code
You can download the full source code of this example
.
This same script is also included in the Nipype source distribution under the
examples
directory.