Apply suggestions from code review

Co-authored-by: Oscar Esteban <[email protected]>

Author: eilidhmacnicol

nirodents/workflows/brainextraction.py

@@ -113,11 +113,9 @@ def init_rodent_brain_extraction_wf(
     mrg_tmpl = pe.Node(niu.Merge(2), name='mrg_tmpl')
     # mrg_tmpl.inputs.in1 = tpl_target_path
 
-    #create integration nodes to allow compatability between pipelines
-    integrate_1 = pe.Node(niu.Function(function=_integrate, 
-        input_names=['in_file'], output_names=['out_file']), name='integrate_1')
-    integrate_2 = pe.Node(niu.Function(function=_integrate, 
-        input_names=['in_file'], output_names=['out_file']), name='integrate_2')
+    # Create integration nodes to allow compatibility between pipelines
+    integrate_1 = pe.Node(niu.IdentityInterface(fields=["in_file"]), name='integrate_1')
+    integrate_2 = pe.Node(niu.IdentityInterface(fields=["in_file"]), name='integrate_2')
 
     # Initialize transforms with antsAI
     init_aff = pe.Node(AI(
@@ -301,7 +299,7 @@ def init_rodent_brain_extraction_wf(
         (warp_mask_out, sinker, [('output_image', 'derivatives.@out_mask')]),
     ])
     # add second target prep stage if necessary
-    if modality.lower == 't2w':
+    if modality.lower() == 't2w':
         wf.connect([(warp_mask_1, tar_prep, [('output_image', 'inu_n4_final.weight_image')])])
 
     # add segmentation if necessary
@@ -343,4 +341,4 @@ def res_by_spc(in_file, out_file = None):
 def _integrate(in_file, out_file = None):
     import os.path as op     
     out_file = op.abspath(in_file)
-    return out_file
+    return out_file