Fixed some connections for eddy outputs

Author: slimnsour

dmriprep/workflows/dwi/base.py

@@ -233,8 +233,8 @@ def _bold_reg_suffix(fallback):
             ("in_bvec", "inputnode.in_bvec"),
             ("in_bval", "inputnode.in_bval")
         ]),
-        (dwi_reference_wf, eddy_report, [("outputnode.dwi_file", "before")]),
-        (eddy_wf, eddy_report, [('outputnode.out_eddy', 'after')]),
+        (dwi_reference_wf, eddy_report, [("outputnode.ref_image", "before")]),
+        (eddy_wf, eddy_report, [('outputnode.eddy_ref_image', 'after')]),
         (dwi_reference_wf, ds_report_eddy, [("outputnode.dwi_file", "source_file")]),
         (eddy_report, ds_report_eddy, [("out_report", "in_file")]),
     ])

dmriprep/workflows/dwi/eddy.py

@@ -77,7 +77,7 @@ def init_eddy_wf(debug=False, name="eddy_wf"):
         The eddy corrected diffusion image..
 
     """
-    from nipype.interfaces.fsl import Eddy
+    from nipype.interfaces.fsl import Eddy, ExtractROI
 
     inputnode = pe.Node(
         niu.IdentityInterface(
@@ -96,6 +96,7 @@ def init_eddy_wf(debug=False, name="eddy_wf"):
         niu.IdentityInterface(
             fields=[
                 "out_rotated_bvecs",
+                "eddy_ref_image",
                 "out_eddy"
             ]
         ),
@@ -127,6 +128,8 @@ def init_eddy_wf(debug=False, name="eddy_wf"):
         name="gen_eddy_files",
     )
 
+    eddy_ref_img = pe.Node(ExtractROI(t_min=0, t_size=1), name="eddy_roi")
+
     # fmt:off
     workflow.connect([
         (inputnode, eddy, [
@@ -147,6 +150,8 @@ def init_eddy_wf(debug=False, name="eddy_wf"):
             ("out_corrected", "out_eddy"),
             ("out_rotated_bvecs", "out_rotated_bvecs")
         ]),
+        (eddy, eddy_ref_img, [("out_corrected", "in_file")]),
+        (eddy_ref_img, outputnode, [("roi_file", "eddy_ref_image")]),
     ])
     # fmt:on
     return workflow