Merge remote-tracking branch 'nipy/master'

Author: tsalo

nipype/algorithms/confounds.py

@@ -208,7 +208,7 @@ def _list_outputs(self):
 
 class FramewiseDisplacementInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc='motion parameters')
-    parameter_source = traits.Enum("FSL", "AFNI", "SPM", "FSFAST",
+    parameter_source = traits.Enum("FSL", "AFNI", "SPM", "FSFAST", "NIPY",
                                    desc="Source of movement parameters",
                                    mandatory=True)
     radius = traits.Float(50, usedefault=True,

nipype/algorithms/modelgen.py

@@ -33,6 +33,7 @@
                                traits, File, Bunch, BaseInterfaceInputSpec,
                                isdefined)
 from ..utils.filemanip import filename_to_list
+from ..utils.misc import normalize_mc_params
 from .. import config, logging
 iflogger = logging.getLogger('interface')
 
@@ -195,6 +196,9 @@ class SpecifyModelInputSpec(BaseInterfaceInputSpec):
                                             desc='Realignment parameters returned '
                                                  'by motion correction algorithm',
                                             copyfile=False)
+    parameter_source = traits.Enum("SPM", "FSL", "AFNI", "FSFAST", "NIPY",
+                                   usedefault=True,
+                                   desc="Source of motion parameters")
     outlier_files = InputMultiPath(File(exists=True),
                                    desc='Files containing scan outlier indices '
                                         'that should be tossed',
@@ -392,8 +396,10 @@ def _generate_design(self, infolist=None):
         realignment_parameters = []
         if isdefined(self.inputs.realignment_parameters):
             for parfile in self.inputs.realignment_parameters:
-                realignment_parameters.append(np.loadtxt(parfile))
-
+                realignment_parameters.append(
+                    np.apply_along_axis(func1d=normalize_mc_params,
+                                        axis=1, arr=np.loadtxt(parfile),
+                                        source=self.inputs.parameter_source))
         outliers = []
         if isdefined(self.inputs.outlier_files):
             for filename in self.inputs.outlier_files:
@@ -556,7 +562,9 @@ def _generate_design(self, infolist=None):
         if isdefined(self.inputs.realignment_parameters):
             realignment_parameters = []
             for parfile in self.inputs.realignment_parameters:
-                mc = np.loadtxt(parfile)
+                mc = np.apply_along_axis(func1d=normalize_mc_params,
+                                         axis=1, arr=np.loadtxt(parfile),
+                                         source=self.inputs.parameter_source)
                 if not realignment_parameters:
                     realignment_parameters.insert(0, mc)
                 else:

nipype/algorithms/tests/test_auto_SpecifyModel.py

@@ -19,6 +19,8 @@ def test_SpecifyModel_inputs():
     ),
     outlier_files=dict(copyfile=False,
     ),
+    parameter_source=dict(usedefault=True,
+    ),
     realignment_parameters=dict(copyfile=False,
     ),
     subject_info=dict(mandatory=True,

nipype/algorithms/tests/test_auto_SpecifySPMModel.py

@@ -23,6 +23,8 @@ def test_SpecifySPMModel_inputs():
     ),
     output_units=dict(usedefault=True,
     ),
+    parameter_source=dict(usedefault=True,
+    ),
     realignment_parameters=dict(copyfile=False,
     ),
     subject_info=dict(mandatory=True,

nipype/algorithms/tests/test_auto_SpecifySparseModel.py

@@ -20,6 +20,8 @@ def test_SpecifySparseModel_inputs():
     model_hrf=dict(),
     outlier_files=dict(copyfile=False,
     ),
+    parameter_source=dict(usedefault=True,
+    ),
     realignment_parameters=dict(copyfile=False,
     ),
     save_plot=dict(),

nipype/utils/misc.py

@@ -248,10 +248,25 @@ def unflatten(in_list, prev_structure):
 def normalize_mc_params(params, source):
     """
     Normalize a single row of motion parameters to the SPM format.
+
+    SPM saves motion parameters as:
+        x   Right-Left          (mm)
+        y   Anterior-Posterior  (mm)
+        z   Superior-Inferior   (mm)
+        rx  Pitch               (rad)
+        ry  Yaw                 (rad)
+        rz  Roll                (rad)
     """
-    if source == 'FSL':
+    if source.upper() == 'FSL':
         params = params[[3, 4, 5, 0, 1, 2]]
-    elif source in ('AFNI', 'FSFAST'):
+    elif source.upper() 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
+    elif source.upper() == 'NIPY':
+        from nipy.algorithms.registration import to_matrix44, aff2euler
+        matrix = to_matrix44(params)
+        params = np.zeros(6)
+        params[:3] = matrix[:3, 3]
+        params[-1:2:-1] = aff2euler(matrix)
+
+    return params