sMRI: Using ANTS for registration

In this simple tutorial we will use the Registration interface from ANTS to coregister two 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 urllib.request
import urllib.error
import urllib.parse
from nipype.interfaces.ants import Registration
from nipype.testing import example_data

  1. Download T1 volumes into home directory

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'),
]
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'),
]

3. Define the parameters of the registration. Settings are found in the file smri_ants_registration_settings.json distributed with the example_data of nipype.

reg = Registration(
    from_file=example_data('smri_ants_registration_settings.json'))
reg.inputs.fixed_image = input_images[0]
reg.inputs.moving_image = input_images[1]

Alternatively to the use of the from_file feature to load ANTs settings, the user can manually set all those inputs instead:

reg.inputs.output_transform_prefix = 'thisTransform'
reg.inputs.output_warped_image = 'INTERNAL_WARPED.nii.gz'
reg.inputs.output_transform_prefix = "output_"
reg.inputs.transforms = ['Translation', 'Rigid', 'Affine', 'SyN']
reg.inputs.transform_parameters = [(0.1,), (0.1,), (0.1,), (0.2, 3.0, 0.0)]
reg.inputs.number_of_iterations = ([[10000, 111110, 11110]] * 3 +
                                   [[100, 50, 30]])
reg.inputs.dimension = 3
reg.inputs.write_composite_transform = True
reg.inputs.collapse_output_transforms = False
reg.inputs.metric = ['Mattes'] * 3 + [['Mattes', 'CC']]
reg.inputs.metric_weight = [1] * 3 + [[0.5, 0.5]]
reg.inputs.radius_or_number_of_bins = [32] * 3 + [[32, 4]]
reg.inputs.sampling_strategy = ['Regular'] * 3 + [[None, None]]
reg.inputs.sampling_percentage = [0.3] * 3 + [[None, None]]
reg.inputs.convergence_threshold = [1.e-8] * 3 + [-0.01]
reg.inputs.convergence_window_size = [20] * 3 + [5]
reg.inputs.smoothing_sigmas = [[4, 2, 1]] * 3 + [[1, 0.5, 0]]
reg.inputs.sigma_units = ['vox'] * 4
reg.inputs.shrink_factors = [[6, 4, 2]] + [[3, 2, 1]] * 2 + [[4, 2, 1]]
reg.inputs.use_estimate_learning_rate_once = [True] * 4
reg.inputs.use_histogram_matching = [False] * 3 + [True]
reg.inputs.initial_moving_transform_com = True

print(reg.cmdline)

  1. Run the registration

reg.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.