Added default trt fallback and eddy reportlet

Author: slimnsour

dmriprep/workflows/dwi/base.py

@@ -69,6 +69,7 @@ def init_dwi_preproc_wf(dwi_file, has_fieldmap=False):
 
     """
     from ...interfaces.vectors import CheckGradientTable
+    from niworkflows.interfaces import SimpleBeforeAfter
     from .util import init_dwi_reference_wf
     from .outputs import init_reportlets_wf
     from .eddy import init_eddy_wf
@@ -205,6 +206,23 @@ def _bold_reg_suffix(fallback):
     # Eddy distortion correction
     eddy_wf = init_eddy_wf(debug=config.execution.debug)
     eddy_wf.inputs.inputnode.metadata = layout.get_metadata(str(dwi_file))
+
+    ds_report_eddy = pe.Node(
+        DerivativesDataSink(
+            base_directory=str(config.execution.output_dir),
+            desc="eddy_corrected",
+            datatype="figures",
+        ),
+        name="ds_report_eddy",
+        run_without_submitting=True,
+    )
+
+    eddy_report = pe.Node(
+        SimpleBeforeAfter(before_label="Distorted", after_label="Eddy Corrected",),
+        name="eddy_report",
+        mem_gb=0.1,
+    )
+
     # fmt:off
     workflow.connect([
         (dwi_reference_wf, eddy_wf, [
@@ -215,6 +233,10 @@ def _bold_reg_suffix(fallback):
             ("in_bvec", "inputnode.in_bvec"),
             ("in_bval", "inputnode.in_bval")
         ]),
+        (dwi_reference_wf, eddy_report, [("outputnode.dwi_file", "before")]),
+        (eddy_wf, eddy_report, [('outputnode.out_eddy', 'after')]),
+        (dwi_reference_wf, ds_report_eddy, [("outputnode.dwi_file", "source_file")]),
+        (eddy_report, ds_report_eddy, [("out_report", "in_file")]),
     ])
     # fmt:on
 

dmriprep/workflows/dwi/eddy.py

@@ -43,9 +43,18 @@ def gen_eddy_textfiles(in_file, in_meta):
     fsl_pe["ijk".index(pe_dir[0])] = "-1" if pe_dir.endswith("-") else "1"
 
     # Write to the acqp file
-    Path(out_acqparams).write_text(
-        f"{' '.join(fsl_pe)} {get_trt(in_meta, in_file=in_file):0.7f}"
-    )
+    try:
+        Path(out_acqparams).write_text(
+            f"{' '.join(fsl_pe)} {get_trt(in_meta, in_file=in_file):0.7f}"
+        )
+    except ValueError:
+        config.loggers.workflow.warning(
+            f"'TotalReadoutTime' not found for <{dwi_file}>, using"
+            f"a default value of 0.05 instead."
+        )
+        Path(out_acqparams).write_text(
+            f"{' '.join(fsl_pe)} {0.05}"
+        )
 
     out_index = fname_presuffix(in_file, suffix="_index.txt", use_ext=False,)
     Path(out_index).write_text(f"{' '.join(['1'] * nb.load(in_file).shape[3])}")