Merge tag '25.2.4'

effigies · effigies · commit 38267950f3b0 · 2026-01-14T13:24:14.000-05:00
25.2.4 (January 14, 2026) Bug-fix release in the 25.2.x series. This release addresses some errors in multi-echo and multi-session processing. * FIX: Set source_file in ds_report* nodes at resampling level (#3590) * FIX: Ravel multi-echo data for BIDSSourceFile with precomputed smriprep (#3583) * FIX: Ensure multi-echo processing and slice timing correction text is in boilerplate (#3577) * FIX: Pass session_id to fieldmap finder (#3573) * FIX: Import LinAlgError from a stable location (#3572) * ENH: Raise error if two-echo data are provided (#3570) * MNT: Prune Ubuntu environment before building docker images (#3571)
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,3 +1,17 @@
+25.2.4 (January 14, 2026)
+=========================
+Bug-fix release in the 25.2.x series.
+
+This release addresses some errors in multi-echo and multi-session processing.
+
+* FIX: Set source_file in ds_report* nodes at resampling level (#3590)
+* FIX: Ravel multi-echo data for BIDSSourceFile with precomputed smriprep (#3583)
+* FIX: Ensure multi-echo processing and slice timing correction text is in boilerplate (#3577)
+* FIX: Pass session_id to fieldmap finder (#3573)
+* FIX: Import LinAlgError from a stable location (#3572)
+* ENH: Raise error if two-echo data are provided (#3570)
+* MNT: Prune Ubuntu environment before building docker images (#3571)
+
 25.2.3 (October 17, 2025)
 =========================
 Bug-fix release in the 25.2.x series.
diff --git a/fmriprep/data/boilerplate.bib b/fmriprep/data/boilerplate.bib
@@ -379,3 +379,16 @@ @article{onavg
 	pages = {1736--1742},
 	doi = {10.1038/s41592-024-02346-y},
 }
+
+@article{DuPre2021,
+    doi = {10.21105/joss.03669},
+    url = {https://doi.org/10.21105/joss.03669},
+    year = {2021},
+    publisher = {The Open Journal},
+    volume = {6},
+    number = {66},
+    pages = {3669},
+    author = {DuPre, Elizabeth and Salo, Taylor and Ahmed, Zaki and Bandettini, Peter A. and Bottenhorn, Katherine L. and Caballero-Gaudes, César and Dowdle, Logan T. and Gonzalez-Castillo, Javier and Heunis, Stephan and Kundu, Prantik and Laird, Angela R. and Markello, Ross and Markiewicz, Christopher J. and Moia, Stefano and Staden, Isla and Teves, Joshua B. and Uruñuela, Eneko and Vaziri-Pashkam, Maryam and Whitaker, Kirstie and Handwerker, Daniel A.},
+    title = {TE-dependent analysis of multi-echo fMRI with *tedana*},
+    journal = {Journal of Open Source Software},
+}
diff --git a/fmriprep/interfaces/bids.py b/fmriprep/interfaces/bids.py
@@ -85,7 +85,7 @@ def _run_interface(self, runtime):
         src = self.inputs.bids_info[self.inputs.anat_type]
 
         if not src and self.inputs.precomputed.get(f'{self.inputs.anat_type}_preproc'):
-            src = self.inputs.bids_info['bold']
+            src = _ravel(self.inputs.bids_info['bold'])
             self._results['source_file'] = _create_multi_source_file(src)
             return runtime
 
diff --git a/fmriprep/interfaces/tests/test_bids.py b/fmriprep/interfaces/tests/test_bids.py
@@ -1,5 +1,7 @@
 """Tests for fmriprep.interfaces.bids."""
 
+import pytest
+
 
 def test_BIDSURI():
     """Test the BIDSURI interface."""
@@ -70,3 +72,62 @@ def test_BIDSURI():
         'bids:deriv-0:sub-01/func/sub-01_task-rest_bold.nii.gz',
         '/out/sub-01/func/sub-01_task-rest_bold.nii.gz',  # No change
     ]
+
+
+bids_infos_anat = [
+    [{'t1w': ['sub-01/anat/sub-01_T1w.nii.gz']}, {}],
+    [{'t2w': ['sub-01/anat/sub-01_T2w.nii.gz']}, {}],
+    [
+        {'t1w': []},
+        {'t1w_preproc': ['sourcedata/smriprep/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz']},
+    ],
+    [
+        {'t2w': []},
+        {'t2w_preproc': ['sourcedata/smriprep/sub-01/anat/sub-01_desc-preproc_T2w.nii.gz']},
+    ],
+]
+
+bids_infos_func = {
+    'single-echo': {
+        'bold': ['sub-01/func/sub-01_task-rest_bold.nii.gz'],
+    },
+    'multi-echo': {
+        'bold': [
+            [
+                'sub-01/func/sub-01_task-rest_echo-1_bold.nii.gz',
+                'sub-01/func/sub-01_task-rest_echo-2_bold.nii.gz',
+                'sub-01/func/sub-01_task-rest_echo-3_bold.nii.gz',
+            ],
+        ],
+    },
+}
+
+
+@pytest.mark.parametrize(
+    ('bids_info_anat', 'bids_info_func', 'precomputed_infos'),
+    [
+        (bids_info_anat, bids_info_func, precomputed_infos)
+        for bids_info_anat, precomputed_infos in bids_infos_anat
+        for func_case, bids_info_func in bids_infos_func.items()
+    ],
+)
+def test_BIDSSourceFile(bids_info_anat, bids_info_func, precomputed_infos):
+    """Test the BIDSSourceFile interface"""
+    from fmriprep.interfaces.bids import BIDSSourceFile
+
+    interface = BIDSSourceFile()
+    anat_type = next(iter(bids_info_anat))
+    interface.inputs.anat_type = anat_type
+    interface.inputs.bids_info = {**bids_info_anat, **bids_info_func}
+    interface.inputs.precomputed = precomputed_infos
+    results = interface.run()
+
+    if precomputed_infos:
+        bold = (
+            'sub-01/func/sub-01_bold.nii.gz'
+            if isinstance(bids_info_func['bold'][0], list)
+            else 'sub-01/func/sub-01_task-rest_bold.nii.gz'
+        )
+        assert results.outputs.source_file == bold
+    else:
+        assert results.outputs.source_file == bids_info_anat[anat_type][0]
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
@@ -374,6 +374,7 @@ def init_bold_wf(
         for node in workflow.list_node_names():
             if node.split('.')[-1].startswith('ds_report'):
                 workflow.get_node(node).inputs.base_directory = fmriprep_dir
+                workflow.get_node(node).inputs.source_file = bold_file
         return workflow
 
     # Pass along BOLD reference as a source file for provenance
diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
@@ -802,6 +802,7 @@ def init_bold_native_wf(
     .. _optimal combination: https://tedana.readthedocs.io/en/stable/approach.html#optimal-combination
 
     """
+    from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
     layout = config.execution.layout
 
@@ -830,7 +831,7 @@ def init_bold_native_wf(
 
     run_stc = bool(metadata.get('SliceTiming')) and 'slicetiming' not in config.workflow.ignore
 
-    workflow = pe.Workflow(name=name)
+    workflow = Workflow(name=name)
 
     inputnode = pe.Node(
         niu.IdentityInterface(
diff --git a/fmriprep/workflows/bold/t2s.py b/fmriprep/workflows/bold/t2s.py
@@ -99,9 +99,9 @@ def init_bold_t2s_wf(
         fit_str = 'log-linear regression'
 
     workflow.__desc__ = f"""\
-A T2<sup>★</sup> map was estimated from the preprocessed EPI echoes, by voxel-wise fitting
-the maximal number of echoes with reliable signal in that voxel to a monoexponential signal
-decay model with {fit_str}.
+A T2<sup>★</sup> map was estimated from the preprocessed EPI echoes using tedana's t2smap
+workflow [@DuPre2021], by voxel-wise fitting the maximal number of echoes with reliable signal in
+that voxel to a monoexponential signal decay model with {fit_str}.
 The calculated T2<sup>★</sup> map was then used to optimally combine preprocessed BOLD across
 echoes following the method described in [@posse_t2s].
 The optimally combined time series was carried forward as the *preprocessed BOLD*.
diff --git a/pixi.lock b/pixi.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -27,7 +27,7 @@ dependencies = [
     "nireports >= 24.1.0",
     "nitime >= 0.9",
     "nitransforms >= 25.0.1",
-    "niworkflows >= 1.14.2",
+    "niworkflows >= 1.14.4",
     "numpy >= 2.0",
     "packaging >= 24",
     "pandas >= 2.2",
