diff --git a/bin/dwifslpreproc b/bin/dwifslpreproc
index 78776ba556..1ec58eb433 100755
--- a/bin/dwifslpreproc
+++ b/bin/dwifslpreproc
@@ -483,7 +483,7 @@ def execute(): #pylint: disable=unused-variable
         overwrite_dwi_pe_scheme = True
     if manual_trt:
       # Compare manual specification to that read from the header
-      if not scheme_times_match(dwi_pe_scheme, dwi_manual_pe_scheme):
+      if len(dwi_pe_scheme[0]) == 4 and app.ARGS.readout_time is not None and not scheme_times_match(dwi_pe_scheme, dwi_manual_pe_scheme):
         app.warn('User-defined total readout time does not match what is stored in DWI image header; proceeding with user specification')
         overwrite_dwi_pe_scheme = True
     if overwrite_dwi_pe_scheme:
@@ -556,7 +556,7 @@ def execute(): #pylint: disable=unused-variable
             app.warn('User-defined phase-encoding direction design does not match what is stored in SE EPI image header; proceeding with user specification')
             overwrite_se_epi_pe_scheme = True
         if manual_trt:
-          if not scheme_times_match(se_epi_pe_scheme, se_epi_manual_pe_scheme):
+          if len(se_epi_pe_scheme[0]) == 4 and not scheme_times_match(se_epi_pe_scheme, se_epi_manual_pe_scheme):
             app.warn('User-defined total readout time does not match what is stored in SE EPI image header; proceeding with user specification')
             overwrite_se_epi_pe_scheme = True
         if overwrite_se_epi_pe_scheme:
diff --git a/testing/scripts/tests/dwifslpreproc b/testing/scripts/tests/dwifslpreproc
index fa3a742d3c..dbc9f3cf58 100644
--- a/testing/scripts/tests/dwifslpreproc
+++ b/testing/scripts/tests/dwifslpreproc
@@ -1,4 +1,5 @@
 mkdir -p ../tmp/dwifslpreproc && mrconvert BIDS/sub-04/dwi/sub-04_dwi.nii.gz -fslgrad BIDS/sub-04/dwi/sub-04_dwi.bvec BIDS/sub-04/dwi/sub-04_dwi.bval -json_import BIDS/sub-04/dwi/sub-04_dwi.json tmp-sub-04_dwi.mif -export_grad_mrtrix tmp-sub-04_dwi.b -strides 0,0,0,1 && dwifslpreproc tmp-sub-04_dwi.mif ../tmp/dwifslpreproc/rpenone_default.mif -pe_dir ap -readout_time 0.1 -rpe_none -force && testing_diff_header ../tmp/dwifslpreproc/rpenone_default.mif dwifslpreproc/rpenone_default.mif.gz
+mrconvert tmp-sub-04_dwi.mif -clear_property TotalReadoutTime tmp-sub-04_trt-none_dwi.mif && dwifslpreproc tmp-sub-04_trt-none ../tmp/dwifslpreproc/no_trt_header.mif -pe_dir ap -readout_time 0.1 -force
 dwifslpreproc BIDS/sub-04/dwi/sub-04_dwi.nii.gz -fslgrad BIDS/sub-04/dwi/sub-04_dwi.bvec BIDS/sub-04/dwi/sub-04_dwi.bval ../tmp/dwifslpreproc/fslgrad.mif -export_grad_fsl ../tmp/dwifslpreproc/fslgrad.bvec ../tmp/dwifslpreproc/fslgrad.bval -pe_dir ap -readout_time 0.1 -rpe_none -force && testing_diff_header ../tmp/dwifslpreproc/fslgrad.mif dwifslpreproc/rpenone_default.mif.gz && testing_diff_matrix ../tmp/dwifslpreproc/fslgrad.bvec dwifslpreproc/rpenone_default.bvec -abs 1e-2 && testing_diff_matrix ../tmp/dwifslpreproc/fslgrad.bval dwifslpreproc/rpenone_default.bval
 dwifslpreproc BIDS/sub-04/dwi/sub-04_dwi.nii.gz -grad tmp-sub-04_dwi.b ../tmp/dwifslpreproc/grad.mif -export_grad_mrtrix ../tmp/dwifslpreproc/grad.b -pe_dir ap -readout_time 0.1 -rpe_none -force && testing_diff_header ../tmp/dwifslpreproc/grad.mif dwifslpreproc/rpenone_default.mif.gz && testing_diff_matrix ../tmp/dwifslpreproc/grad.b dwifslpreproc/rpenone_default.b -abs 1e-2
 mrconvert BIDS/sub-04/fmap/sub-04_dir-1_epi.nii.gz -json_import BIDS/sub-04/fmap/sub-04_dir-1_epi.json tmp-sub-04_dir-1_epi.mif -force && mrconvert BIDS/sub-04/fmap/sub-04_dir-2_epi.nii.gz -json_import BIDS/sub-04/fmap/sub-04_dir-2_epi.json tmp-sub-04_dir-2_epi.mif -force && mrcat tmp-sub-04_dir-1_epi.mif tmp-sub-04_dir-2_epi.mif tmp-sub-04_dir-all_epi.mif -axis 3 -force && dwifslpreproc tmp-sub-04_dwi.mif ../tmp/dwifslpreproc/rpepair_default.mif -pe_dir ap -readout_time 0.1 -rpe_pair -se_epi tmp-sub-04_dir-all_epi.mif -force && testing_diff_header ../tmp/dwifslpreproc/rpepair_default.mif dwifslpreproc/rpepair_default.mif.gz