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# sMRI: Using new ANTS for creating a T1 template

In this tutorial we will use ANTS (old version aka “ANTS”) based workflow to create a template out of multiple T1 volumes.

1. 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 ANTSTemplateBuildSingleIterationWF

2. 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))

    input_images=[
    os.path.join(mydatadir,'01_T1_half.nii.gz'),
    os.path.join(mydatadir,'02_T1_half.nii.gz'),
    os.path.join(mydatadir,'03_T1_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')}
    ]

3. Define the workflow and its working directory

    tbuilder=pe.Workflow(name="ANTSTemplateBuilder")
    tbuilder.base_dir=requestedPath

4. Define data sources. In real life these would be replace by DataGrabbers

    datasource = pe.Node(interface=util.IdentityInterface(fields=
                        ['imageList', 'passiveImagesDictionariesList']),
                        run_without_submitting=True,
                        name='InputImages' )
    datasource.inputs.imageList=input_images
    datasource.inputs.passiveImagesDictionariesList=input_passive_images
    datasource.inputs.sort_filelist = True

5. Template is initialized by a simple average

    initAvg = pe.Node(interface=ants.AverageImages(), name ='initAvg')
    initAvg.inputs.dimension = 3
    initAvg.inputs.normalize = True

    tbuilder.connect(datasource, "imageList", initAvg, "images")

6. Define the first iteration of template building

    buildTemplateIteration1=ANTSTemplateBuildSingleIterationWF('iteration01')
    tbuilder.connect(initAvg, 'output_average_image', buildTemplateIteration1, 'inputspec.fixed_image')
    tbuilder.connect(datasource, 'imageList', buildTemplateIteration1, 'inputspec.images')
    tbuilder.connect(datasource, 'passiveImagesDictionariesList', buildTemplateIteration1, 'inputspec.ListOfPassiveImagesDictionaries')

7. Define the second iteration of template building

    buildTemplateIteration2 = ANTSTemplateBuildSingleIterationWF('iteration02')
    tbuilder.connect(buildTemplateIteration1, 'outputspec.template', buildTemplateIteration2, 'inputspec.fixed_image')
    tbuilder.connect(datasource, 'imageList', buildTemplateIteration2, 'inputspec.images')
    tbuilder.connect(datasource, 'passiveImagesDictionariesList', buildTemplateIteration2, 'inputspec.ListOfPassiveImagesDictionaries')

8. 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')

8. Run the workflow

    tbuilder.run()

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.