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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.

    from __future__ import print_function, unicode_literals
    from builtins import open
    from future import standard_library
    standard_library.install_aliases()

    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 urllib.request
    import urllib.error
    import urllib.parse
    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 = urllib.request.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.