Merge pull request #1840 from chrisfilo/enh/fd_afni

Support for motion parameters produced by AFNI (FD)

Author: chrisgorgo

nipype/algorithms/confounds.py

@@ -27,7 +27,8 @@
 from ..interfaces.base import (traits, TraitedSpec, BaseInterface,
                                BaseInterfaceInputSpec, File, isdefined,
                                InputMultiPath)
-from nipype.utils import NUMPY_MMAP
+from ..utils import NUMPY_MMAP
+from ..utils.misc import normalize_mc_params
 
 IFLOG = logging.getLogger('interface')
 
@@ -206,7 +207,10 @@ 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')
+    parameter_source = traits.Enum("FSL", "AFNI", "SPM", "FSFAST",
+                                   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')
@@ -260,9 +264,12 @@ class FramewiseDisplacement(BaseInterface):
     }]
 
     def _run_interface(self, runtime):
-        mpars = np.loadtxt(self.inputs.in_plots)  # mpars is N_t x 6
-        diff = mpars[:-1, :] - mpars[1:, :]
-        diff[:, :3] *= self.inputs.radius
+        mpars = np.loadtxt(self.inputs.in_file)  # mpars is N_t x 6
+        mpars = np.apply_along_axis(func1d=normalize_mc_params,
+                                    axis=1, arr=mpars,
+                                    source=self.inputs.parameter_source)
+        diff = mpars[:-1, :6] - mpars[1:, :6]
+        diff[:, 3:6] *= self.inputs.radius
         fd_res = np.abs(diff).sum(axis=1)
 
         self._results = {

nipype/algorithms/rapidart.py

@@ -34,7 +34,7 @@
                                OutputMultiPath, TraitedSpec, File,
                                BaseInterfaceInputSpec, isdefined)
 from ..utils.filemanip import filename_to_list, save_json, split_filename
-from ..utils.misc import find_indices
+from ..utils.misc import find_indices, normalize_mc_params
 from .. import logging, config
 iflogger = logging.getLogger('interface')
 
@@ -46,15 +46,12 @@ def _get_affine_matrix(params, source):
     source : the package that generated the parameters
              supports SPM, AFNI, FSFAST, FSL, NIPY
     """
-    if source == 'FSL':
-        params = params[[3, 4, 5, 0, 1, 2]]
-    elif source in ('AFNI', 'FSFAST'):
-        params = params[np.asarray([4, 5, 3, 1, 2, 0]) + (len(params) > 6)]
-        params[3:] = params[3:] * np.pi / 180.
     if source == 'NIPY':
         # nipy does not store typical euler angles, use nipy to convert
         from nipy.algorithms.registration import to_matrix44
         return to_matrix44(params)
+
+    params = normalize_mc_params(params, source)
     # process for FSL, SPM, AFNI and FSFAST
     rotfunc = lambda x: np.array([[np.cos(x), np.sin(x)],
                                   [-np.sin(x), np.cos(x)]])

nipype/algorithms/tests/test_auto_FramewiseDisplacement.py

@@ -11,7 +11,7 @@ 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,
     ),

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

nipype/utils/misc.py

@@ -243,3 +243,15 @@ def unflatten(in_list, prev_structure):
         for item in prev_structure:
             out.append(unflatten(in_list, item))
         return out
+
+
+def normalize_mc_params(params, source):
+    """
+    Normalize a single row of motion parameters to the SPM format.
+    """
+    if source == 'FSL':
+        params = params[[3, 4, 5, 0, 1, 2]]
+    elif source in ('AFNI', 'FSFAST'):
+        params = params[np.asarray([4, 5, 3, 1, 2, 0]) + (len(params) > 6)]
+        params[3:] = params[3:] * np.pi / 180.
+    return params