Update outputs.py

xcp_d/workflows/outputs.py

@@ -11,7 +11,7 @@
 from xcp_d.interfaces.utils import FilterUndefined
 from xcp_d.utils.bids import get_entity
 from xcp_d.utils.doc import fill_doc
-from xcp_d.utils.utils import _make_dictionary, _out_file_to_source
+from xcp_d.utils.utils import _make_dictionary
 
 
 @fill_doc
@@ -281,10 +281,14 @@ def init_postproc_derivatives_wf(
         name="outputnode",
     )
 
-    def _postproc_to_source(out_file):
+    def _postproc_to_source(out_file, output_dir):
+        from xcp_d.utils.utils import _out_file_to_source
+
         return _out_file_to_source(out_file, "xcp_d", os.path.join(output_dir, "xcp_d"))
 
-    def _preproc_to_source(out_file):
+    def _preproc_to_source(out_file, fmri_dir):
+        from xcp_d.utils.utils import _out_file_to_source
+
         return _out_file_to_source(out_file, "preprocessed", fmri_dir)
 
     # Create dictionary of basic information
@@ -316,7 +320,7 @@ def _preproc_to_source(out_file):
     # Determine cohort (if there is one) in the original data
     cohort = get_entity(name_source, "cohort")
 
-    preproc_bold_src = _preproc_to_source(name_source)
+    preproc_bold_src = _preproc_to_source(name_source, fmri_dir)
 
     preproc_confounds_src = pe.Node(
         InferBIDSURIs(
@@ -409,7 +413,9 @@ def _preproc_to_source(out_file):
             ("temporal_mask_metadata", "meta_dict"),
             ("temporal_mask", "in_file"),
         ]),
-        (ds_filtered_motion, ds_temporal_mask, [(("out_file", _postproc_to_source), "Sources")]),
+        (ds_filtered_motion, ds_temporal_mask, [
+            (("out_file", _postproc_to_source, output_dir), "Sources"),
+        ]),
         (ds_temporal_mask, outputnode, [("out_file", "temporal_mask")]),
     ])
     # fmt:on
@@ -485,7 +491,7 @@ def _preproc_to_source(out_file):
                 ("interpolated_filtered_bold", "in_file"),
             ]),
             (ds_denoised_bold, ds_interpolated_denoised_bold, [
-                (("out_file", _postproc_to_source), "Sources"),
+                (("out_file", _postproc_to_source, output_dir), "Sources"),
             ]),
             (ds_interpolated_denoised_bold, outputnode, [
                 ("out_file", "interpolated_filtered_bold"),
@@ -535,7 +541,7 @@ def _preproc_to_source(out_file):
     workflow.connect([
         (make_atlas_dict, add_denoised_to_src, [("metadata", "metadata")]),
         (ds_denoised_bold, add_denoised_to_src, [
-            (("out_file", _postproc_to_source), "Sources"),
+            (("out_file", _postproc_to_source, output_dir), "Sources"),
         ]),
     ])
     # fmt:on
@@ -563,7 +569,9 @@ def _preproc_to_source(out_file):
         # fmt:off
         workflow.connect([
             (inputnode, ds_smoothed_bold, [("smoothed_denoised_bold", "in_file")]),
-            (ds_denoised_bold, ds_smoothed_bold, [(("out_file", _postproc_to_source), "Sources")]),
+            (ds_denoised_bold, ds_smoothed_bold, [
+                (("out_file", _postproc_to_source, output_dir), "Sources"),
+            ]),
             (ds_smoothed_bold, outputnode, [("out_file", "smoothed_denoised_bold")]),
         ])
         # fmt:on
@@ -609,7 +617,7 @@ def _preproc_to_source(out_file):
     workflow.connect([
         (add_denoised_to_src, add_coverage_to_src, [("metadata", "metadata")]),
         (ds_coverage, add_coverage_to_src, [
-            (("out_file", _postproc_to_source), "Sources"),
+            (("out_file", _postproc_to_source, output_dir), "Sources"),
         ]),
     ])
     # fmt:on
@@ -718,7 +726,7 @@ def _preproc_to_source(out_file):
         workflow.connect([
             (add_denoised_to_src, add_ccoverage_to_src, [("metadata", "metadata")]),
             (ds_coverage_ciftis, add_ccoverage_to_src, [
-                (("out_file", _postproc_to_source), "Sources"),
+                (("out_file", _postproc_to_source, output_dir), "Sources"),
             ]),
         ])
         # fmt:on
@@ -851,7 +859,7 @@ def _preproc_to_source(out_file):
     # fmt:off
     workflow.connect([
         (inputnode, ds_reho, [("reho", "in_file")]),
-        (ds_denoised_bold, ds_reho, [(("out_file", _postproc_to_source), "Sources")]),
+        (ds_denoised_bold, ds_reho, [(("out_file", _postproc_to_source, output_dir), "Sources")]),
     ])
     # fmt:on
 
@@ -870,7 +878,7 @@ def _preproc_to_source(out_file):
     # fmt:off
     workflow.connect([
         (make_atlas_dict, add_reho_to_src, [("metadata", "metadata")]),
-        (ds_reho, add_reho_to_src, [(("out_file", _postproc_to_source), "Sources")]),
+        (ds_reho, add_reho_to_src, [(("out_file", _postproc_to_source, output_dir), "Sources")]),
     ])
     # fmt:on
 
@@ -922,7 +930,9 @@ def _preproc_to_source(out_file):
         # fmt:off
         workflow.connect([
             (inputnode, ds_alff, [("alff", "in_file")]),
-            (ds_denoised_bold, ds_alff, [(("out_file", _postproc_to_source), "Sources")]),
+            (ds_denoised_bold, ds_alff, [
+                (("out_file", _postproc_to_source, output_dir), "Sources"),
+            ]),
         ])
         # fmt:on
 
@@ -949,7 +959,9 @@ def _preproc_to_source(out_file):
             # fmt:off
             workflow.connect([
                 (inputnode, ds_smoothed_alff, [("smoothed_alff", "in_file")]),
-                (ds_alff, ds_smoothed_alff, [(("out_file", _postproc_to_source), "Sources")]),
+                (ds_alff, ds_smoothed_alff, [
+                    (("out_file", _postproc_to_source, output_dir), "Sources"),
+                ]),
             ])
             # fmt:on
 
@@ -967,7 +979,9 @@ def _preproc_to_source(out_file):
         # fmt:off
         workflow.connect([
             (make_atlas_dict, add_alff_to_src, [("metadata", "metadata")]),
-            (ds_alff, add_alff_to_src, [(("out_file", _postproc_to_source), "Sources")]),
+            (ds_alff, add_alff_to_src, [
+                (("out_file", _postproc_to_source, output_dir), "Sources"),
+            ]),
         ])
         # fmt:on