Improve QC method for FUGUE fieldmap correction

pni-lab · Jan 17, 2025 · da50825 · da50825
1 parent 8c20823
commit da50825
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/PUMI/pipelines/func/deconfound.py b/PUMI/pipelines/func/deconfound.py
@@ -41,13 +41,16 @@ def create_fieldmap_plot(overlay, background):
     overlay_vol = pick_volume('overlay_vol', overlay_volume)
     wf.connect('inputspec', 'overlay', overlay_vol, 'in_file')
 
+    overlay_bet = bet_deepbet('overlay_bet')
+    wf.connect(overlay_vol, 'out_file', overlay_bet, 'in_file')
+
     plot = Node(Function(input_names=['overlay', 'background'],
                          output_names=['out_file'],
                          function=create_fieldmap_plot),
                 name='plot')
 
     wf.connect('inputspec', 'background', plot, 'background')
-    wf.connect(overlay_vol, 'out_file', plot, 'overlay')
+    wf.connect(overlay_bet, 'out_file', plot, 'overlay')
 
     wf.connect(plot, 'out_file', 'sinker', 'qc_fieldmap_correction')