From 42e66fa13f2ef255df8a9545f96015896f4888c3 Mon Sep 17 00:00:00 2001
From: Logan Bennett <logben@stanford.edu>
Date: Sat, 25 Apr 2026 14:24:54 -0700
Subject: [PATCH 1/2] FIX: Remove redundant fmap_boldref resample in fmapCoreg
 report

The 'fieldmap' input to init_func_fit_reports_wf is supplied by
boldref_fmap (fit.py:500), which already reconstructs the fieldmap onto
the BOLD reference grid. The fmap_boldref ApplyTransforms node added in
gh-3387 was correct at the time but became redundant after gh-3467
rewired the input to come from boldref_fmap.

The redundant resample applies boldref2fmap_xfm (inverted) to data
already in BOLD space, shifting the fieldmap overlay in
desc-fmapCoreg_bold.svg by ||boldref2fmap_xfm||. For acquisitions
where BOLD and fieldmap have similar FOV anchors, the visible shift is
within the brain and the figure looks fine; for acquisitions with
substantially different FOV anchors (e.g. fieldmap reusing functional
prescription with slice thickness/spacing decoupled), the overlay can
render entirely outside the brain.

The actual SDC correction is unaffected: unwarp_boldref (fit.py:614)
and the time-series resample in apply.py both use ReconstructFieldmap
outputs directly without going through fmap_boldref.
---
 fmriprep/workflows/bold/outputs.py | 19 +------------------
 1 file changed, 1 insertion(+), 18 deletions(-)

diff --git a/fmriprep/workflows/bold/outputs.py b/fmriprep/workflows/bold/outputs.py
index df8de999c..8eae813cd 100644
--- a/fmriprep/workflows/bold/outputs.py
+++ b/fmriprep/workflows/bold/outputs.py
@@ -313,18 +313,6 @@ def init_func_fit_reports_wf(
             mem_gb=1,
         )
 
-        fmap_boldref = pe.Node(
-            ApplyTransforms(
-                dimension=3,
-                default_value=0,
-                float=True,
-                invert_transform_flags=[True],
-                interpolation='LanczosWindowedSinc',
-            ),
-            name='fmap_boldref',
-            mem_gb=1,
-        )
-
         # SDC1
         sdcreg_report = pe.Node(
             FieldmapReportlet(
@@ -377,17 +365,12 @@ def init_func_fit_reports_wf(
                 ('coreg_boldref', 'reference_image'),
                 ('boldref2fmap_xfm', 'transforms'),
             ]),
-            (inputnode, fmap_boldref, [
-                ('fieldmap', 'input_image'),
-                ('coreg_boldref', 'reference_image'),
-                ('boldref2fmap_xfm', 'transforms'),
-            ]),
             (inputnode, sdcreg_report, [
                 ('sdc_boldref', 'reference'),
+                ('fieldmap', 'fieldmap'),
                 ('bold_mask', 'mask'),
             ]),
             (fmapref_boldref, sdcreg_report, [('output_image', 'moving')]),
-            (fmap_boldref, sdcreg_report, [('output_image', 'fieldmap')]),
             (sdcreg_report, ds_sdcreg_report, [('out_report', 'in_file')]),
             (inputnode, sdc_report, [
                 ('sdc_boldref', 'before'),

From 8b7b3acb1cd7f7ad33f21b0457e8f4a85e47a209 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 13 May 2026 10:06:05 -0400
Subject: [PATCH 2/2] doc: Update inputs for init_func_fit_reports_wf

---
 fmriprep/workflows/bold/outputs.py | 36 ++++++++++++++++++------------
 1 file changed, 22 insertions(+), 14 deletions(-)

diff --git a/fmriprep/workflows/bold/outputs.py b/fmriprep/workflows/bold/outputs.py
index 8eae813cd..f8c9ebbb3 100644
--- a/fmriprep/workflows/bold/outputs.py
+++ b/fmriprep/workflows/bold/outputs.py
@@ -163,25 +163,33 @@ def init_func_fit_reports_wf(
 
     Inputs
     ------
-    std_t1w
-        T1w image resampled to standard space
-    std_mask
-        Mask of skull-stripped template
-    subject_dir
-        FreeSurfer SUBJECTS_DIR
-    subject_id
-        FreeSurfer subject ID
-    t1w_conform_report
-        Conformation report
+    sdc_boldref
+        BOLD reference before SDC, in BOLD space
+    coreg_boldref
+        BOLD reference after SDC, in BOLD space
+    boldref2anat_xfm
+        Affine transform from BOLD reference to anatomical space
+    boldref2fmap_xfm
+        Affine transform from BOLD reference to fieldmap space
     t1w_preproc
         The T1w reference map, which is calculated as the average of bias-corrected
         and preprocessed T1w images, defining the anatomical space.
-    t1w_dseg
-        Segmentation in T1w space
     t1w_mask
         Brain (binary) mask estimated by brain extraction.
-    template
-        Template space and specifications
+    t1w_dseg
+        Segmentation in T1w space
+    fieldmap
+        Reconstructed fieldmap, in BOLD space
+    fmap_ref
+        Fieldmap reference image, in fieldmap space
+    subject_dir
+        FreeSurfer SUBJECTS_DIR
+    subject_id
+        FreeSurfer subject ID
+    summary_report
+        HTML snippet summarizing BOLD processing decisions
+    validation_report
+        HTML snippet indicating whether affine metadata were overwritten
 
     """
     from nireports.interfaces.reporting.base import (