adedd support for motion parameters produced by AFNI

Author: chrisgorgo

nipype/algorithms/confounds.py

@@ -195,7 +195,8 @@ 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')
+    format = traits.Enum("FSL", "AFNI", desc="Format of the motion parameters file: FSL (radians), AFNI (degrees)")
     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')
@@ -249,9 +250,11 @@ 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.format == "AFNI":
+            diff[:, :3] *= (np.pi / 180)
         fd_res = np.abs(diff).sum(axis=1)
 
         self._results = {

nipype/algorithms/tests/test_confounds.py

@@ -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',
+                                          format="FSL")
     res = fdisplacement.run()
 
     with open(res.outputs.out_file) as all_lines: