FIX: Ensure connections and names make sense

nipreps · Oct 15, 2023 · 4564048 · 4564048
1 parent d2fcd38
commit 4564048
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Showing 2 changed files with 15 additions and 12 deletions.
diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
@@ -229,8 +229,10 @@ def init_bold_fit_wf(
     # fmt:off
     workflow.connect([
         (hmcref_buffer, outputnode, [("boldref", "hmc_boldref")]),
-        (regref_buffer, outputnode, [("boldref", "coreg_boldref"),
-                                     ("boldmask", "bold_mask")]),
+        (regref_buffer, outputnode, [
+            ("boldref", "coreg_boldref"),
+            ("boldmask", "bold_mask"),
+        ]),
         (fmapreg_buffer, outputnode, [("boldref2fmap_xfm", "boldref2fmap_xfm")]),
         (hmc_buffer, outputnode, [("hmc_xforms", "motion_xfm")]),
         (inputnode, func_fit_reports_wf, [
@@ -556,6 +558,7 @@ def init_bold_native_wf(
             fields=[
                 # BOLD fit
                 "boldref",
+                "bold_mask",
                 "motion_xfm",
                 "fmapreg_xfm",
                 "dummy_scans",

diff --git a/fmriprep/workflows/bold/outputs.py b/fmriprep/workflows/bold/outputs.py
@@ -588,7 +588,7 @@ def init_ds_bold_native_wf(
     workflow.connect(inputnode, 'source_files', raw_sources, 'in_files')
 
     if bold_output:
-        ds_bold_native = pe.Node(
+        ds_bold = pe.Node(
             DerivativesDataSink(
                 base_directory=output_dir,
                 desc='preproc',
@@ -598,36 +598,36 @@ def init_ds_bold_native_wf(
                 dismiss_entities=("echo",),
                 **timing_parameters,
             ),
-            name='ds_bold_native',
+            name='ds_bold',
             run_without_submitting=True,
             mem_gb=DEFAULT_MEMORY_MIN_GB,
         )
         workflow.connect([
-            (inputnode, ds_bold_native, [
+            (inputnode, ds_bold, [
                 ('source_files', 'source_file'),
-                ('bold_native', 'in_file'),
+                ('bold', 'in_file'),
             ]),
         ])  # fmt:skip
 
     if bold_output or echo_output:
-        ds_bold_mask_native = pe.Node(
+        ds_bold_mask = pe.Node(
             DerivativesDataSink(
                 base_directory=output_dir,
                 desc='brain',
                 suffix='mask',
                 compress=True,
                 dismiss_entities=("echo",),
             ),
-            name='ds_bold_mask_native',
+            name='ds_bold_mask',
             run_without_submitting=True,
             mem_gb=DEFAULT_MEMORY_MIN_GB,
         )
         workflow.connect([
-            (inputnode, ds_bold_mask_native, [
+            (inputnode, ds_bold_mask, [
                 ('source_files', 'source_file'),
-                ('bold_mask_native', 'in_file'),
+                ('bold_mask', 'in_file'),
             ]),
-            (raw_sources, ds_bold_mask_native, [('out', 'RawSources')]),
+            (raw_sources, ds_bold_mask, [('out', 'RawSources')]),
         ])  # fmt:skip
 
     if bold_output and multiecho:
@@ -676,7 +676,7 @@ def init_ds_bold_native_wf(
         workflow.connect([
             (inputnode, ds_bold_echos, [
                 ('source_files', 'source_file'),
-                ('bold_echos_native', 'in_file'),
+                ('bold_echos', 'in_file'),
             ]),
         ])  # fmt:skip