def calc_fd(mat_file, dataset="fnl"):
"""
Compute Framewise Displacement as in Power et al 2012 and save to file. Uses the default radius of 50mm.
Args:
mat_file (path object): .mat file outputted from FSL
dataset (str): 'fnl' or 'sherlock'
Returns:
file_path
"""
assert isinstance(mat_file, Path), "realigned_series must be a Path object"
out_file = mat_file.parent / "fd_power_2012.csv"
fd = FramewiseDisplacement(
in_file=mat_file, out_file=out_file, parameter_source="FSL", save_plot=False
)
if dataset == "fnl":
fd.inputs.series_tr = 2.0
elif dataset == "sherlock":
fd.inputs.series_tr = 1.5
_ = fd.run()
return out_file
def test_fd():
tempdir = mkdtemp()
ground_truth = np.loadtxt(example_data('fsl_motion_outliers_fd.txt'))
fd = FramewiseDisplacement(in_plots=example_data('fsl_mcflirt_movpar.txt'),
out_file=tempdir + '/fd.txt')
res = fd.run()
yield assert_equal, np.allclose(ground_truth, np.loadtxt(res.outputs.out_file)), True
yield assert_equal, np.abs(ground_truth.mean() - res.outputs.fd_average) < 1e-4, True
rmtree(tempdir)
def test_fd(tmpdir):
tempdir = str(tmpdir)
ground_truth = np.loadtxt(example_data('fsl_motion_outliers_fd.txt'))
fdisplacement = FramewiseDisplacement(in_plots=example_data('fsl_mcflirt_movpar.txt'),
out_file=tempdir + '/fd.txt')
res = fdisplacement.run()
with open(res.outputs.out_file) as all_lines:
for line in all_lines:
assert 'FramewiseDisplacement' in line
break
assert np.allclose(ground_truth, np.loadtxt(res.outputs.out_file, skiprows=1), atol=.16)
assert np.abs(ground_truth.mean() - res.outputs.fd_average) < 1e-2
def test_fd():
tempdir = mkdtemp()
ground_truth = np.loadtxt(example_data('fsl_motion_outliers_fd.txt'))
fdisplacement = FramewiseDisplacement(
in_plots=example_data('fsl_mcflirt_movpar.txt'),
out_file=tempdir + '/fd.txt')
res = fdisplacement.run()
yield assert_true, np.allclose(ground_truth,
np.loadtxt(res.outputs.out_file),
atol=.16)
yield assert_true, np.abs(ground_truth.mean() -
res.outputs.fd_average) < 1e-2
rmtree(tempdir)
def test_fd():
tempdir = mkdtemp()
ground_truth = np.loadtxt(example_data('fsl_motion_outliers_fd.txt'))
fdisplacement = FramewiseDisplacement(in_plots=example_data('fsl_mcflirt_movpar.txt'),
out_file=tempdir + '/fd.txt')
res = fdisplacement.run()
with open(res.outputs.out_file) as all_lines:
for line in all_lines:
yield assert_in, 'framewise_displacement', line
break
yield assert_true, np.allclose(ground_truth, np.loadtxt(res.outputs.out_file), atol=.16)
yield assert_true, np.abs(ground_truth.mean() - res.outputs.fd_average) < 1e-2
rmtree(tempdir)
def test_fd(tmpdir):
tempdir = str(tmpdir)
ground_truth = np.loadtxt(example_data('fsl_motion_outliers_fd.txt'))
fdisplacement = FramewiseDisplacement(
in_plots=example_data('fsl_mcflirt_movpar.txt'),
out_file=tempdir + '/fd.txt')
res = fdisplacement.run()
with open(res.outputs.out_file) as all_lines:
for line in all_lines:
assert 'FramewiseDisplacement' in line
break
assert np.allclose(ground_truth,
np.loadtxt(res.outputs.out_file, skiprows=1),
atol=.16)
assert np.abs(ground_truth.mean() - res.outputs.fd_average) < 1e-2
def test_fd(tmpdir):
tempdir = tmpdir.strpath
ground_truth = np.loadtxt(example_data("fsl_motion_outliers_fd.txt"))
fdisplacement = FramewiseDisplacement(
in_file=example_data("fsl_mcflirt_movpar.txt"),
out_file=tempdir + "/fd.txt",
parameter_source="FSL",
)
res = fdisplacement.run()
with open(res.outputs.out_file) as all_lines:
for line in all_lines:
assert "FramewiseDisplacement" in line
break
assert np.allclose(ground_truth,
np.loadtxt(res.outputs.out_file, skiprows=1),
atol=0.16)
assert np.abs(ground_truth.mean() - res.outputs.fd_average) < 1e-2
