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dwifslpreproc: Fix for PE direction, but not readout time, in header #2722

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Merged
Lestropie merged 1 commit into from
Feb 6, 2025
Merged

dwifslpreproc: Fix for PE direction, but not readout time, in header #2722

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4 changes: 2 additions & 2 deletions bin/dwifslpreproc
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -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:
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1 change: 1 addition & 0 deletions testing/scripts/tests/dwifslpreproc
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@@ -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
Expand Down