ENH: Improve fieldmap support (#205)

* MAINT: Bump black to avoid click dependency issues

* ENH: Add flag to control maximum volumes topup uses

* FIX: Re-enable reverse-PE EPI fieldmaps

Co-authored by: Christopher J. Markiewicz <[email protected]>

Author: mgxd

.pre-commit-config.yaml

@@ -7,6 +7,6 @@ repos:
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black
-    rev: 22.1.0
+    rev: 22.3.0
     hooks:
     -   id: black

nibabies/cli/parser.py

@@ -442,6 +442,12 @@ def _slice_time_ref(value, parser):
         default=True,
         help="do not remove median (within mask) from fieldmap",
     )
+    g_fmap.add_argument(
+        "--topup-max-vols",
+        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")

nibabies/config.py

@@ -557,6 +557,8 @@ 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 = False

nibabies/workflows/base.py

@@ -484,21 +484,20 @@ def init_single_subject_wf(subject_id):
         if estimator.method in (fm.EstimatorType.MAPPED, fm.EstimatorType.PHASEDIFF):
             continue
 
-        suffices = set(s.suffix for s in estimator.sources)
-
-        if estimator.method == fm.EstimatorType.PEPOLAR and sorted(suffices) == ["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
-            ]
-            continue
+        suffices = [s.suffix for s in estimator.sources]
 
         if estimator.method == fm.EstimatorType.PEPOLAR:
-            raise NotImplementedError(
-                "Sophisticated PEPOLAR schemes (e.g., using DWI+EPI) are unsupported."
-            )
+            if set(suffices) == {"epi"} or sorted(suffices) == ["bold", "epi"]:
+                fmap_wf_inputs = getattr(fmap_wf.inputs, f"in_{estimator.bids_id}")
+                fmap_wf_inputs.in_data = [str(s.path) for s in estimator.sources]
+                fmap_wf_inputs.metadata = [s.metadata for s in estimator.sources]
+
+                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 (e.g., using DWI+EPI) are unsupported."
+                )
 
     return workflow