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.
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
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')
}]
Define the workflow and its working directory
tbuilder = pe.Workflow(name="ANTSTemplateBuilder")
tbuilder.base_dir = requestedPath
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
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")
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')
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')
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')
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.