FIX: Only connect template_iterator_wf if it exists

Author: effigies

fmriprep/workflows/base.py

@@ -333,6 +333,7 @@ def init_single_subject_wf(subject_id: str):
     ])  # fmt:skip
 
     # Set up the template iterator once, if used
+    template_iterator_wf = None
     if config.workflow.level == "full":
         if spaces.cached.get_spaces(nonstandard=False, dim=(3,)):
             template_iterator_wf = init_template_iterator_wf(spaces=spaces)
@@ -556,16 +557,17 @@ def init_single_subject_wf(subject_id: str):
             ])  # fmt:skip
 
         if config.workflow.level == "full":
-            workflow.connect([
-                (template_iterator_wf, bold_wf, [
-                    ("outputnode.anat2std_xfm", "inputnode.anat2std_xfm"),
-                    ("outputnode.space", "inputnode.std_space"),
-                    ("outputnode.resolution", "inputnode.std_resolution"),
-                    ("outputnode.cohort", "inputnode.std_cohort"),
-                    ("outputnode.std_t1w", "inputnode.std_t1w"),
-                    ("outputnode.std_mask", "inputnode.std_mask"),
-                ]),
-            ])  # fmt:skip
+            if template_iterator_wf is not None:
+                workflow.connect([
+                    (template_iterator_wf, bold_wf, [
+                        ("outputnode.anat2std_xfm", "inputnode.anat2std_xfm"),
+                        ("outputnode.space", "inputnode.std_space"),
+                        ("outputnode.resolution", "inputnode.std_resolution"),
+                        ("outputnode.cohort", "inputnode.std_cohort"),
+                        ("outputnode.std_t1w", "inputnode.std_t1w"),
+                        ("outputnode.std_mask", "inputnode.std_mask"),
+                    ]),
+                ])  # fmt:skip
 
             # Thread MNI152NLin6Asym standard outputs to CIFTI subworkflow, skipping
             # the iterator, which targets only output spaces.

fmriprep/workflows/bold/base.py

@@ -54,6 +54,7 @@
     init_ds_registration_wf,
     init_ds_volumes_wf,
     init_func_derivatives_wf,
+    prepare_timing_parameters,
 )
 from .registration import init_bold_reg_wf, init_bold_t1_trans_wf
 from .resampling import (
@@ -399,7 +400,7 @@ def init_bold_wf(
             (bold_anat_wf, ds_bold_t1_wf, [('outputnode.bold_file', 'inputnode.bold')]),
         ])  # fmt:skip
 
-    if spaces.get_spaces(nonstandard=False, dim=(3,)):
+    if spaces.cached.get_spaces(nonstandard=False, dim=(3,)):
         # Missing:
         #  * Clipping BOLD after resampling
         #  * Resampling parcellations
@@ -495,6 +496,21 @@ def init_bold_wf(
             repetition_time=all_metadata[0]["RepetitionTime"],
         )
 
+        ds_bold_cifti = pe.Node(
+            DerivativesDataSink(
+                base_directory=fmriprep_dir,
+                space='fsLR',
+                density=config.workflow.cifti_output,
+                suffix='bold',
+                compress=False,
+                TaskName=all_metadata[0].get('TaskName'),
+                **prepare_timing_parameters(all_metadata[0]),
+            ),
+            name='ds_bold_cifti',
+            run_without_submitting=True,
+        )
+        ds_bold_cifti.inputs.source_file = bold_file
+
         workflow.connect([
             # Resample BOLD to MNI152NLin6Asym, may duplicate bold_std_wf above
             (inputnode, bold_MNI6_wf, [
@@ -532,6 +548,10 @@ def init_bold_wf(
             (bold_fsLR_resampling_wf, bold_grayords_wf, [
                 ("outputnode.bold_fsLR", "inputnode.bold_fsLR"),
             ]),
+            (bold_grayords_wf, ds_bold_cifti, [
+                ('outputnode.cifti_bold', 'in_file'),
+                (('outputnode.cifti_metadata', _read_json), 'meta_dict'),
+            ]),
         ])  # fmt:skip
 
     bold_confounds_wf = init_bold_confs_wf(
@@ -975,3 +995,10 @@ def get_img_orientation(imgf):
     """Return the image orientation as a string"""
     img = nb.load(imgf)
     return "".join(nb.aff2axcodes(img.affine))
+
+
+def _read_json(in_file):
+    from json import loads
+    from pathlib import Path
+
+    return loads(Path(in_file).read_text())

fmriprep/workflows/bold/outputs.py

@@ -982,30 +982,6 @@ def init_func_derivatives_wf(
         ])
         # fmt:on
 
-    # CIFTI output
-    if cifti_output:
-        ds_bold_cifti = pe.Node(
-            DerivativesDataSink(
-                base_directory=output_dir,
-                suffix='bold',
-                compress=False,
-                TaskName=metadata.get('TaskName'),
-                space='fsLR',
-                **timing_parameters,
-            ),
-            name='ds_bold_cifti',
-            run_without_submitting=True,
-            mem_gb=DEFAULT_MEMORY_MIN_GB,
-        )
-        # fmt:off
-        workflow.connect([
-            (inputnode, ds_bold_cifti, [(('bold_cifti', _unlist), 'in_file'),
-                                        ('source_file', 'source_file'),
-                                        ('cifti_density', 'density'),
-                                        (('cifti_metadata', _read_json), 'meta_dict')])
-        ])
-        # fmt:on
-
     if "compcor" in config.execution.debug:
         ds_acompcor_masks = pe.Node(
             DerivativesDataSink(
@@ -1120,10 +1096,3 @@ def _unlist(in_file):
     while isinstance(in_file, (list, tuple)) and len(in_file) == 1:
         in_file = in_file[0]
     return in_file
-
-
-def _read_json(in_file):
-    from json import loads
-    from pathlib import Path
-
-    return loads(Path(in_file).read_text())