Merge tag '23.1.4'

23.1.4 (August 1, 2023)

Patch release in the 23.1.x series.

This release prioritizes single-band reference BOLD images during SyN-SDC schemes.
Additionally, an indices inconsistency was fixed for CIFTI volumetric data.

* FIX: Pass sbref files to SyN workflow (#3060)
* FIX: Generate CIFTI volume structure indices in column-major order (nipreps/niworkflows#815)

CHANGES.rst

@@ -1,3 +1,14 @@
+23.1.4 (August 1, 2023)
+=======================
+Patch release in the 23.1.x series.
+
+This release prioritizes single-band reference BOLD images during SyN-SDC schemes.
+Additionally, an indices inconsistency was fixed for CIFTI volumetric data.
+
+* FIX: Pass sbref files to SyN workflow (#3060)
+* FIX: Generate CIFTI volume structure indices in column-major order (nipreps/niworkflows#815)
+
+
 23.1.3 (June 24, 2023)
 ======================
 

fmriprep/workflows/base.py

@@ -428,10 +428,20 @@ def init_single_subject_wf(subject_id: str):
 
             fmap_estimators = [fmap for fmap in fmap_estimators if fmap.bids_id in used_estimators]
 
+            # Simplification: Unused estimators are removed from registry
+            # This fiddles with a private attribute, so it may break in future
+            # versions. However, it does mean the BOLD workflow doesn't need to
+            # replicate the logic that got us to the pared down set of estimators
+            # here.
+            final_ids = {fmap.bids_id for fmap in fmap_estimators}
+            unused_ids = fm._estimators.keys() - final_ids
+            for bids_id in unused_ids:
+                del fm._estimators[bids_id]
+
         if fmap_estimators:
             config.loggers.workflow.info(
                 "B0 field inhomogeneity map will be estimated with "
-                f" the following {len(fmap_estimators)} estimators: "
+                f"the following {len(fmap_estimators)} estimator(s): "
                 f"{[e.method for e in fmap_estimators]}."
             )
 
@@ -562,8 +572,8 @@ def init_single_subject_wf(subject_id: str):
         elif estimator.method == fm.EstimatorType.ANAT:
             from sdcflows.workflows.fit.syn import init_syn_preprocessing_wf
 
-            sources = [str(s.path) for s in estimator.sources if s.suffix == "bold"]
-            source_meta = [s.metadata for s in estimator.sources if s.suffix == "bold"]
+            sources = [str(s.path) for s in estimator.sources if s.suffix in ("bold", "sbref")]
+            source_meta = [s.metadata for s in estimator.sources if s.suffix in ("bold", "sbref")]
             syn_preprocessing_wf = init_syn_preprocessing_wf(
                 omp_nthreads=config.nipype.omp_nthreads,
                 debug=config.execution.sloppy,

fmriprep/workflows/bold/base.py

@@ -289,7 +289,14 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
     config.loggers.workflow.info(sbref_msg)
 
     if has_fieldmap:
-        estimator_key = get_estimator(layout, bold_file if not multiecho else bold_file[0])
+        from sdcflows import fieldmaps as fm
+
+        # We may have pruned the estimator collection due to `--ignore fieldmaps`
+        estimator_key = [
+            key
+            for key in get_estimator(layout, bold_file if not multiecho else bold_file[0])
+            if key in fm._estimators
+        ]
 
         if not estimator_key:
             has_fieldmap = False

requirements.txt

@@ -143,7 +143,7 @@ nitransforms==22.0.0
     #   fmriprep (pyproject.toml)
     #   niworkflows
     #   sdcflows
-niworkflows==1.8.0
+niworkflows==1.8.1
     # via
     #   fmriprep (pyproject.toml)
     #   sdcflows