debug tcompcor, add log messages and tests

Author: Shoshana Berleant

nipype/algorithms/confounds.py

@@ -420,11 +420,13 @@ def _run_interface(self, runtime):
         threshold_index = int(num_voxels * (1. - self.inputs.percentile_threshold))
         threshold_std = sortSTD[threshold_index]
         mask = tSTD >= threshold_std
-        mask = mask.astype(int)
+        mask = mask.astype(int).T
 
         # save mask
         mask_file = 'mask.nii'
         nb.nifti1.save(nb.Nifti1Image(mask, np.eye(4)), mask_file)
+        IFLOG.debug('tCompcor computed and saved mask of shape {} to mask_file {}'
+                   .format(mask.shape, mask_file))
         self.inputs.mask_file = mask_file
 
         super(TCompCor, self)._run_interface(runtime)
@@ -513,6 +515,8 @@ def regress_poly(degree, data, remove_mean=True, axis=-1):
     If remove_mean is True (default), the data is demeaned (i.e. degree 0).
     If remove_mean is false, the data is not.
     '''
+    IFLOG.debug('Performing polynomial regression on data of shape ' + str(data.shape))
+
     datashape = data.shape
     timepoints = datashape[axis]
 

nipype/algorithms/tests/test_compcor.py

@@ -74,6 +74,14 @@ def test_compcor_no_regress_poly(self):
                                                       ['-0.5367548139', '0.0059943226'],
                                                       ['-0.0520809054', '0.2940637551']])
 
+    def test_tcompcor_asymmetric_dim(self):
+        asymmetric_shape = (2, 3, 4, 5)
+        asymmetric_data = utils.save_toy_nii(np.zeros(asymmetric_shape), 'asymmetric.nii')
+
+        TCompCor(realigned_file=asymmetric_data).run()
+
+        self.assertEqual(nb.load('mask.nii').get_data().shape, asymmetric_shape[:3])
+
     def run_cc(self, ccinterface, expected_components):
         # run
         ccresult = ccinterface.run()