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 niflow.nipype1.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 Nipype1 Examples Niflow under the package/niflow/nipype1/examples directory.