Merge pull request #1057 from nathanntg/rsfmri-example-singular

FIX Constant column in motion regressor causes singular matrix

Author: satra

examples/rsfmri_vol_surface_preprocessing.py

@@ -230,7 +230,7 @@ def build_filter1(motion_params, comp_norm, outliers, detrend_poly=None):
             out_params = np.hstack((out_params, outlier_vector))
         if detrend_poly:
             timepoints = out_params.shape[0]
-            X = np.ones((timepoints, 1))
+            X = np.empty((timepoints, 0))
             for i in range(detrend_poly):
                 X = np.hstack((X, legendre(
                     i + 1)(np.linspace(-1, 1, timepoints))[:, None]))
@@ -542,7 +542,7 @@ def create_reg_workflow(name='registration'):
 
     warpmean = Node(ants.ApplyTransforms(), name='warpmean')
     warpmean.inputs.input_image_type = 3
-    warpmean.inputs.interpolation = 'BSpline'
+    warpmean.inputs.interpolation = 'Linear'
     warpmean.inputs.invert_transform_flags = [False, False]
     warpmean.inputs.terminal_output = 'file'
     warpmean.inputs.args = '--float'
@@ -771,7 +771,7 @@ def merge_files(in1, in2):
     warpall = MapNode(ants.ApplyTransforms(), iterfield=['input_image'],
                       name='warpall')
     warpall.inputs.input_image_type = 3
-    warpall.inputs.interpolation = 'BSpline'
+    warpall.inputs.interpolation = 'Linear'
     warpall.inputs.invert_transform_flags = [False, False]
     warpall.inputs.terminal_output = 'file'
     warpall.inputs.reference_image = target_file

examples/rsfmri_vol_surface_preprocessing_nipy.py

@@ -217,7 +217,7 @@ def build_filter1(motion_params, comp_norm, outliers, detrend_poly=None):
             out_params = np.hstack((out_params, outlier_vector))
         if detrend_poly:
             timepoints = out_params.shape[0]
-            X = np.ones((timepoints, 1))
+            X = np.empty((timepoints, 0))
             for i in range(detrend_poly):
                 X = np.hstack((X, legendre(
                     i + 1)(np.linspace(-1, 1, timepoints))[:, None]))
@@ -526,7 +526,7 @@ def create_reg_workflow(name='registration'):
     """
     warpmean = Node(ants.ApplyTransforms(), name='warpmean')
     warpmean.inputs.input_image_type = 3
-    warpmean.inputs.interpolation = 'BSpline'
+    warpmean.inputs.interpolation = 'Linear'
     warpmean.inputs.invert_transform_flags = [False, False]
     warpmean.inputs.terminal_output = 'file'
     warpmean.inputs.args = '--float'
@@ -749,7 +749,7 @@ def merge_files(in1, in2):
     warpall = MapNode(ants.ApplyTransforms(), iterfield=['input_image'],
                       name='warpall')
     warpall.inputs.input_image_type = 3
-    warpall.inputs.interpolation = 'BSpline'
+    warpall.inputs.interpolation = 'Linear'
     warpall.inputs.invert_transform_flags = [False, False]
     warpall.inputs.terminal_output = 'file'
     warpall.inputs.reference_image = target_file