diff --git a/fsl/wrappers/eddy.py b/fsl/wrappers/eddy.py
index 53a90b9ca263984a1be1b168f6ea6a2c02e4e865..27570d1fa6aedbf4ed8e6d624a77bc3a1826c638 100644
--- a/fsl/wrappers/eddy.py
+++ b/fsl/wrappers/eddy.py
@@ -92,7 +92,8 @@ def applytopup(imain, datain, index, **kwargs):
     }
 
     asrt.assertFileExists(datain)
-    asrt.assertIsNifti(imain)
+    for fn in imain.split(','):
+        asrt.assertIsNifti(fn)
 
     cmd  = [
         'applytopup', '--imain={}'.format(imain),