Merge pull request #2688 from effigies/enh/max_trs

ENH: Add --topup-max-vols flag to control TOPUP runtime

fmriprep/cli/parser.py

@@ -481,6 +481,13 @@ def _slice_time_ref(value, parser):
         default=True,
         help="do not remove median (within mask) from fieldmap",
     )
+    g_fmap.add_argument(
+        "--topup-max-vols",
+        action="store",
+        default=5,
+        type=int,
+        help="maximum number of volumes to use with TOPUP, per-series (EPI or BOLD)",
+    )
 
     # SyN-unwarp options
     g_syn = parser.add_argument_group("Specific options for SyN distortion correction")

fmriprep/config.py

@@ -569,6 +569,8 @@ class workflow(_Config):
     spaces = None
     """Keeps the :py:class:`~niworkflows.utils.spaces.SpatialReferences`
     instance keeping standard and nonstandard spaces."""
+    topup_max_vols = 5
+    """Maximum number of volumes to use with TOPUP, per-series (EPI or BOLD)."""
     use_aroma = None
     """Run ICA-:abbr:`AROMA (automatic removal of motion artifacts)`."""
     use_bbr = None

fmriprep/workflows/base.py

@@ -461,12 +461,14 @@ def init_single_subject_wf(subject_id):
 
         if estimator.method == fm.EstimatorType.PEPOLAR:
             if set(suffices) == {"epi"} or sorted(suffices) == ["bold", "epi"]:
-                getattr(fmap_wf.inputs, f"in_{estimator.bids_id}").in_data = [
-                    str(s.path) for s in estimator.sources
-                ]
-                getattr(fmap_wf.inputs, f"in_{estimator.bids_id}").metadata = [
-                    s.metadata for s in estimator.sources
-                ]
+                wf_inputs = getattr(fmap_wf.inputs, f"in_{estimator.bids_id}")
+                wf_inputs.in_data = [str(s.path) for s in estimator.sources]
+                wf_inputs.metadata = [s.metadata for s in estimator.sources]
+
+                # 21.0.x hack to change the number of volumes used
+                # The default of 50 takes excessively long
+                flatten = fmap_wf.get_node(f"wf_{estimator.bids_id}.flatten")
+                flatten.inputs.max_trs = config.workflow.topup_max_vols
             else:
                 raise NotImplementedError(
                     "Sophisticated PEPOLAR schemes are unsupported."