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.
Replacement for erroneous commit faf0788.
Also includes additional test that results in an unhandled exception on 3.0.4 but executes successfully with this change.

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]) == 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:
@@ -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]) == 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:

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