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Support for motion parameters produced by AFNI (FD) #1840

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Merged
merged 4 commits into from
Feb 24, 2017
Merged

Support for motion parameters produced by AFNI (FD) #1840

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febf69d
adedd support for motion parameters produced by AFNI
chrisgorgo Feb 23, 2017
7e8d871
fix auto tests
chrisgorgo Feb 23, 2017
2e2dac1
rename inputs to conform with RapidArt
chrisgorgo Feb 23, 2017
ff2160a
refactor
chrisgorgo Feb 24, 2017
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9 changes: 7 additions & 2 deletions nipype/algorithms/confounds.py
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Original file line number Diff line number Diff line change
Expand Up @@ -195,7 +195,10 @@ def _list_outputs(self):


class FramewiseDisplacementInputSpec(BaseInterfaceInputSpec):
in_plots = File(exists=True, mandatory=True, desc='motion parameters as written by FSL MCFLIRT')
in_file = File(exists=True, mandatory=True, desc='motion parameters as written by FSL MCFLIRT or AFNI 3dvolreg')
parameter_source = traits.Enum("FSL", "AFNI",
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FSFAST can be supported pretty easily, given AFNI support. See other comment. And I believe SPM and FSL parameter files are the same?

desc="Source of movement parameters",
mandatory=True)
radius = traits.Float(50, usedefault=True,
desc='radius in mm to calculate angular FDs, 50mm is the '
'default since it is used in Power et al. 2012')
Expand Down Expand Up @@ -249,9 +252,11 @@ class FramewiseDisplacement(BaseInterface):
}]

def _run_interface(self, runtime):
mpars = np.loadtxt(self.inputs.in_plots) # mpars is N_t x 6
mpars = np.loadtxt(self.inputs.in_file) # mpars is N_t x 6
diff = mpars[:-1, :] - mpars[1:, :]
diff[:, :3] *= self.inputs.radius
if self.inputs.parameter_source == "AFNI":
diff[:, :3] *= (np.pi / 180)
fd_res = np.abs(diff).sum(axis=1)
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I'd suggest modifying the mpars rather than the diff, just to make it a little clearer what's going on. Following also adds FSFAST support.

mpars = np.loadtxt(self.inputs.in_file)  # mpars is N_t x 6 (N_t x 7 for FSFAST)
if self.inputs.parameter_source in ('AFNI', 'FSFAST'):
    mpars = mpars[np.asarray([4, 5, 3, 1, 2, 0]) + (mpars.shape[1] > 6)]
    mpars[:, 3:] *= np.pi / 180
diff = np.diff(mpars, axis=0)
diff[:, :3] *= self.inputs.radius
fd_res = np.abs(diff).sum(axis=1)

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UGH. Do not use the above, which re-sorts the parameters. This can be done more simply by taking the last 6 columns.

mpars = np.loadtxt(self.inputs.in_file)[:, -6:]  # mpars is N_t x 6
if self.inputs.parameter_source in ('AFNI', 'FSFAST'):
    mpars[:, :3] *= np.pi / 180
diff = np.diff(mpars, axis=0)
diff[:, :3] *= self.inputs.radius
fd_res = np.abs(diff).sum(axis=1)

And this doesn't handle SPM, contra my previous comment, because SPM puts its rotation parameters first. (Though my confused comments may support the idea of solving the "load normalized motion params" issue once and reusing.)


self._results = {
Expand Down
2 changes: 1 addition & 1 deletion nipype/algorithms/tests/test_auto_FramewiseDisplacement.py
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Expand Up @@ -10,7 +10,7 @@ def test_FramewiseDisplacement_inputs():
ignore_exception=dict(nohash=True,
usedefault=True,
),
in_plots=dict(mandatory=True,
in_file=dict(mandatory=True,
),
normalize=dict(usedefault=True,
),
Expand Down
5 changes: 3 additions & 2 deletions nipype/algorithms/tests/test_confounds.py
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Expand Up @@ -21,8 +21,9 @@
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')
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:
Expand Down