diff --git a/nipype/interfaces/fsl/model.py b/nipype/interfaces/fsl/model.py
index 5571c8066e..055858a9cb 100644
--- a/nipype/interfaces/fsl/model.py
+++ b/nipype/interfaces/fsl/model.py
@@ -349,7 +349,11 @@ def _run_interface(self, runtime):
                                                       self.inputs.contrasts,
                                                       do_tempfilter, basis_key)
             nim = load(func_files[i])
-            (_, _, _, timepoints) = nim.shape
+            if hasattr(nim, 'get_arrays_from_intent'):
+                timepoints = len(
+                    nim.get_arrays_from_intent('NIFTI_INTENT_TIME_SERIES'))
+            else:
+                (_, _, _, timepoints) = nim.shape
             fsf_txt = fsf_header.substitute(
                 run_num=i,
                 interscan_interval=self.inputs.interscan_interval,