dwifslpreproc: Fix for PE direction, but not readout time, in header

If the phase encoding information present in the header is only the phase encoding direction, but not readout time is present, then the constructed phase encoding matrix will possess only three columns, not four. If this happens, but an attempt is then made to cross-reference the readout time in the phase encoding table generated from header content against what the user has specified at the command-line, then an unhandled exception will occur. This change prevents specifically the comparison of readout times from being made if no such information is present.

bin/dwifslpreproc

@@ -476,7 +476,7 @@ 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]) == 3 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:
@@ -549,7 +549,7 @@ 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]) == 3 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: