def test_dilation(fsl_output_type=None):
prev_type = set_output_type(fsl_output_type)
files, testdir, origdir, out_ext = create_files_in_directory()
# Get the command
diller = fsl.DilateImage(in_file="a.nii", out_file="b.nii")
# Test the underlying command
yield assert_equal, diller.cmd, "fslmaths"
# Test that the dilation operation is mandatory
yield assert_raises, ValueError, diller.run
# Test the different dilation operations
for op in ["mean", "modal", "max"]:
cv = dict(mean="M", modal="D", max="F")
diller.inputs.operation = op
yield assert_equal, diller.cmdline, "fslmaths a.nii -dil%s b.nii" % cv[
op]
# Now test the different kernel options
for k in ["3D", "2D", "box", "boxv", "gauss", "sphere"]:
for size in [1, 1.5, 5]:
diller.inputs.kernel_shape = k
diller.inputs.kernel_size = size
yield assert_equal, diller.cmdline, "fslmaths a.nii -kernel %s %.4f -dilF b.nii" % (
k, size)
# Test that we can use a file kernel
f = open("kernel.txt", "w").close()
del f # Shut pyflakes up
diller.inputs.kernel_shape = "file"
diller.inputs.kernel_size = Undefined
diller.inputs.kernel_file = "kernel.txt"
yield assert_equal, diller.cmdline, "fslmaths a.nii -kernel file kernel.txt -dilF b.nii"
# Test that we don't need to request an out name
dil = fsl.DilateImage(in_file="a.nii", operation="max")
yield assert_equal, dil.cmdline, "fslmaths a.nii -dilF %s" % os.path.join(
testdir, "a_dil%s" % out_ext)
# Clean up our mess
clean_directory(testdir, origdir)
set_output_type(prev_type)
def test_dilation(create_files_in_directory_plus_output_type):
files, testdir, out_ext = create_files_in_directory_plus_output_type
# Get the command
diller = fsl.DilateImage(in_file="a.nii", out_file="b.nii")
# Test the underlying command
assert diller.cmd == "fslmaths"
# Test that the dilation operation is mandatory
with pytest.raises(ValueError):
diller.run()
# Test the different dilation operations
for op in ["mean", "modal", "max"]:
cv = dict(mean="M", modal="D", max="F")
diller.inputs.operation = op
assert diller.cmdline == "fslmaths a.nii -dil{} b.nii".format(cv[op])
# Now test the different kernel options
for k in ["3D", "2D", "box", "boxv", "gauss", "sphere"]:
for size in [1, 1.5, 5]:
diller.inputs.kernel_shape = k
diller.inputs.kernel_size = size
assert (diller.cmdline ==
"fslmaths a.nii -kernel {} {:.4f} -dilF b.nii".format(
k, size))
# Test that we can use a file kernel
f = open("kernel.txt", "w").close()
del f # Shut pyflakes up
diller.inputs.kernel_shape = "file"
diller.inputs.kernel_size = Undefined
diller.inputs.kernel_file = "kernel.txt"
assert diller.cmdline == "fslmaths a.nii -kernel file kernel.txt -dilF b.nii"
# Test that we don't need to request an out name
dil = fsl.DilateImage(in_file="a.nii", operation="max")
assert dil.cmdline == "fslmaths a.nii -dilF {}".format(
os.path.join(testdir, "a_dil{}".format(out_ext)))
#Node: Smooth - The volume smoothing option performs a standard SPM smoothing
volsmooth = pe.Node(interface=spm.Smooth(), name = "volsmooth")
volsmooth.inputs.fwhm = 6
#Node: FreeSurferSource - The get specific files from the freesurfer folder
fssource = pe.Node(interface=nio.FreeSurferSource(),name='fssource')
fssource.inputs.subjects_dir = subjects_dir
#Node: Binarize - to binarize the aseg file for the dilation
binarize = pe.Node(interface=fs.Binarize(),name='binarize')
binarize.inputs.min = 0.5
binarize.inputs.out_type = 'nii'
#Node: DilateImage - to dilate the binarized aseg file and use it as a mask
dilate = pe.Node(interface=math.DilateImage(),name='dilate')
dilate.inputs.operation = 'max'
dilate.inputs.output_type = 'NIFTI'
#Connect up the preprocessing components
preproc.connect([(sliceTiming, realign,[('timecorrected_files', 'in_files')]),
(realign, bbregister,[('mean_image', 'source_file')]),
(realign, volsmooth, [('realigned_files', 'in_files')]),
(realign, art,[('realignment_parameters','realignment_parameters'),
('mean_image', 'mask_file'),
]),
(volsmooth,art,[('smoothed_files','realigned_files'),
]),
(fssource, binarize, [('aseg','in_file')]),
(binarize, dilate,[('binary_file','in_file')]),
(realign, art,[('realignment_parameters','realignment_parameters'),