From 375ce6e9d85ae8be4a9c74771062471b310abe1d Mon Sep 17 00:00:00 2001
From: Taylor Salo <salot@pennmedicine.upenn.edu>
Date: Sun, 12 Jan 2025 09:51:24 -0500
Subject: [PATCH] Start addressing review.

---
 src/fmripost_aroma/workflows/base.py     | 15 ---------------
 src/fmripost_aroma/workflows/resample.py | 23 +++++++++++++++++------
 2 files changed, 17 insertions(+), 21 deletions(-)

diff --git a/src/fmripost_aroma/workflows/base.py b/src/fmripost_aroma/workflows/base.py
index ad50b19..828b664 100644
--- a/src/fmripost_aroma/workflows/base.py
+++ b/src/fmripost_aroma/workflows/base.py
@@ -486,20 +486,6 @@ def init_single_run_wf(bold_file):
         bold_MNI6_wf.inputs.inputnode.target_mask = mni6_mask
         bold_MNI6_wf.inputs.inputnode.target_ref_file = mni6_mask
 
-        # Warp desc-preproc_fieldmap to boldref space
-        # Warp the mask as well
-        fieldmap_to_boldref = pe.Node(
-            ApplyTransforms(),
-            name='fieldmap_to_boldref',
-        )
-        workflow.connect([
-            (inputnode, fieldmap_to_boldref, [
-                ('fmap', 'input_image'),  # XXX: not right
-                ('fmap2boldref', 'transforms'),
-                ('bold_mask_native', 'reference_image'),
-            ]),
-        ])  # fmt:skip
-
         # Pass transforms and warped fieldmap to bold_MNI6_wf
         workflow.connect([
             (inputnode, bold_MNI6_wf, [
@@ -510,7 +496,6 @@ def init_single_run_wf(bold_file):
                 # use mask as boldref?
                 ('bold_mask_native', 'inputnode.bold_ref_file'),
             ]),
-            (fieldmap_to_boldref, bold_MNI6_wf, [('output_image', 'fmap')]),
             # Resample BOLD to MNI152NLin6Asym, may duplicate bold_std_wf above
             (stc_buffer, bold_MNI6_wf, [('bold_file', 'inputnode.bold_file')]),
             (bold_MNI6_wf, mni6_buffer, [('outputnode.bold_file', 'bold')]),
diff --git a/src/fmripost_aroma/workflows/resample.py b/src/fmripost_aroma/workflows/resample.py
index 43d6d59..0f2279d 100644
--- a/src/fmripost_aroma/workflows/resample.py
+++ b/src/fmripost_aroma/workflows/resample.py
@@ -4,7 +4,6 @@
 import nipype.pipeline.engine as pe
 from fmriprep.interfaces.resampling import DistortionParameters, ResampleSeries
 from niworkflows.interfaces.nibabel import GenerateSamplingReference
-from niworkflows.interfaces.utility import KeySelect
 
 
 def init_bold_volumetric_resample_wf(
@@ -81,6 +80,8 @@ def init_bold_volumetric_resample_wf(
         further images into the BOLD series' space.
 
     """
+    from fmripost_aroma.interfaces.misc import ApplyTransforms
+
     workflow = pe.Workflow(name=name)
 
     inputnode = pe.Node(
@@ -145,19 +146,29 @@ def init_bold_volumetric_resample_wf(
     if not fieldmap_id:
         return workflow
 
+    # Warp desc-preproc_fieldmap to boldref space
+    # Warp the mask as well
+    fieldmap_to_boldref = pe.Node(
+        ApplyTransforms(),
+        name='fieldmap_to_boldref',
+    )
+    workflow.connect([
+        (inputnode, fieldmap_to_boldref, [
+            ('fmap', 'input_image'),  # XXX: not right
+            ('fmap2boldref', 'transforms'),
+            ('bold_mask_native', 'reference_image'),
+        ]),
+    ])  # fmt:skip
+
     distortion_params = pe.Node(
         DistortionParameters(metadata=metadata),
         name='distortion_params',
         run_without_submitting=True,
     )
     workflow.connect([
-        (inputnode, fmap_select, [
-            ('fmap', 'fmap_ref'),
-            ('fmap_id', 'keys'),
-        ]),
         (inputnode, distortion_params, [('bold_file', 'in_file')]),
         # Inject fieldmap correction into resample node
-        (fmap_select, resample, [('fmap', 'fieldmap')]),
+        (fieldmap_to_boldref, resample, [('fmap', 'fieldmap')]),
         (distortion_params, resample, [
             ('readout_time', 'ro_time'),
             ('pe_direction', 'pe_dir'),