Propagate b0 threshold to dwibiascorrect

PennLINC · Feb 29, 2024 · 71fe6ca · 71fe6ca
1 parent 999512f
commit 71fe6ca
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Showing 2 changed files with 10 additions and 2 deletions.
diff --git a/qsiprep/interfaces/mrtrix.py b/qsiprep/interfaces/mrtrix.py
@@ -1170,6 +1170,10 @@ class DWIBiasCorrectInputSpec(MRTrix3BaseInputSpec, SeriesPreprocReportInputSpec
     ants_c = traits.Str(default_value="[200x200,1e-6]", argstr="-ants.c %s", usedefault=True)
     ants_s = traits.Str(default_value="4", argstr="-ants.s %s")
     out_report = File("n4_report.svg", usedefault=True, desc="filename for the visual report")
+    bzero_max = traits.Int(
+        argstr="-config BZeroThreshold %d",
+        desc="Maximum b-value that can be considered a b=0",
+    )
 
 
 class DWIBiasCorrectOutputSpec(SeriesPreprocReportOutputSpec):

diff --git a/qsiprep/workflows/dwi/finalize.py b/qsiprep/workflows/dwi/finalize.py
@@ -285,6 +285,7 @@ def init_dwi_finalize_wf(
         name="final_denoise_wf",
         omp_nthreads=omp_nthreads,
         source_file=source_file,
+        b0_threshold=b0_threshold,
         do_biascorr=do_biascorr and write_derivatives,
         num_dwi_acquisitions=len(all_dwis),
     )
@@ -474,6 +475,7 @@ def init_finalize_denoising_wf(
     omp_nthreads,
     source_file,
     do_biascorr,
+    b0_threshold,
     num_dwi_acquisitions,
     split_biascorr=False,
     do_patch2self=False,
@@ -532,7 +534,9 @@ def init_finalize_denoising_wf(
     if do_biascorr:
         if not split_biascorr:
             biascorr = pe.Node(
-                DWIBiasCorrect(method="ants"), name="biascorr", n_procs=omp_nthreads
+                DWIBiasCorrect(method="ants", bzero_max=b0_threshold),
+                name="biascorr",
+                n_procs=omp_nthreads,
             )
             ds_report_biascorr = pe.Node(
                 DerivativesDataSink(suffix=name + "_biascorr", source_file=source_file),
@@ -577,7 +581,7 @@ def init_finalize_denoising_wf(
                 scan_num += 1
                 biascorrs.append(
                     pe.Node(
-                        DWIBiasCorrect(method="ants"),
+                        DWIBiasCorrect(method="ants", bzero_max=b0_threshold),
                         name="biascorr%d" % scan_num,
                         n_procs=omp_nthreads,
                     )