Home · Quickstart · Documentation · Citation · NiPy

# 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.

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 antsRegistrationTemplateBuildSingleIterationWF

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))

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'}

3. Define the workflow and its working directory

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

4. 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

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

    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')

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')

9. 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.