ENH: Support flexible CIFTI combinations

fmriprep/config.py

@@ -818,8 +818,31 @@ def init_spaces(checkpoint=True):
     cifti_output = workflow.cifti_output
     if cifti_output:
         # CIFTI grayordinates to corresponding FSL-MNI resolutions.
-        vol_res = '2' if cifti_output == '91k' else '1'
-        spaces.add(Reference('MNI152NLin6Asym', {'res': vol_res}))
+        res = '2' if cifti_output == '91k' else '1'
+        den = '32k' if cifti_output == '91k' else '59k'
+        spaces.add(Reference('fsLR', {'den': den, 'volspace': 'MNI152NLin6Asym', 'volres': res}))
+
+    if spaces.get_spaces(cifti=(True,)):
+        # Figure out the surface spaces and volume spaces we need
+        cifti_spaces = spaces.get_standard(cifti=(True,)) + spaces.get_nonstandard(cifti=(True,))
+        for cifti_space in cifti_spaces:
+            # The surface space
+            spaces.add(
+                Reference(
+                    cifti_space.space,
+                    {k: v for k, v in cifti_space.spec.items() if not k.startswith('vol')},
+                ),
+            )
+            # The volume space
+            spaces.add(
+                Reference(
+                    cifti_space.spec['volspace'],
+                    {
+                        k: v for k, v in cifti_space.spec.items()
+                        if (k.startswith('vol') and k != 'volspace')
+                    },
+                ),
+            )
 
     # Make the SpatialReferences object available
     workflow.spaces = spaces

fmriprep/workflows/bold/base.py

@@ -695,7 +695,7 @@ def init_bold_wf(
             name='carpetplot_wf',
         )
 
-        if config.workflow.cifti_output:
+        if spaces.get_spaces(cifti=(True,)):
             workflow.connect(
                 bold_grayords_wf, 'outputnode.cifti_bold', carpetplot_wf, 'inputnode.cifti_bold',
             )  # fmt:skip