Use get_n_slices() instead of get_dim_info().

Author: Adam Richie-Halford

dmriprep/run.py

@@ -407,7 +407,8 @@ def num_outliers(scan, outliers):
             return len([d for d in outliers if d['scan'] == scan])
 
         if 0 < threshold < 1:
-            threshold *= nib.load(dwi_file).shape[2]
+            img = nib.load(dwi_file)
+            threshold *= img.shape[img.header.get_n_slices()]
 
         drop_scans = np.array([
             s for s in scans
@@ -488,7 +489,9 @@ def drop_outliers_fn(in_file, in_bval, in_bvec, drop_scans):
 
         img = nib.load(op.abspath(in_file))
         img_data = img.get_fdata()
-        img_data_thinned = np.delete(img_data, drop_scans, axis=3)
+        img_data_thinned = np.delete(img_data,
+                                     drop_scans,
+                                     axis=3)
         if isinstance(img, nib.nifti1.Nifti1Image):
             img_thinned = nib.Nifti1Image(img_data_thinned.astype(np.float64),
                                           img.affine,