diff --git a/fmriprep/config.py b/fmriprep/config.py
index 31107991..cc0363a0 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -815,25 +815,34 @@ def init_spaces(checkpoint=True):
     # Ensure user-defined spatial references for outputs are correctly parsed.
     # Certain options require normalization to a space not explicitly defined by users.
     # These spaces will not be included in the final outputs.
-    if cifti_output == '91k':
-        spaces.add(
-            Reference('fsLR', {'den': '32k', 'volspace': 'MNI152NLin6Asym', 'volres': '2'})
-        )
-    elif cifti_output == '170k':
-        spaces.add(
-            Reference('fsLR', {'den': '32k', 'volspace': 'MNI152NLin6Asym', 'volres': '1'})
-        )
+    cifti_output = workflow.cifti_output
+    if cifti_output:
+        # CIFTI grayordinates to corresponding FSL-MNI resolutions.
+        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,))
+        cifti_spaces = spaces.get_standard(cifti=(True,)) + spaces.get_nonstandard(cifti=(True,))
         for cifti_space in cifti_spaces:
-            surface_space = cifti_space
-            volume_space = cifti_space
-
-        # CIFTI grayordinates to corresponding FSL-MNI resolutions.
-        vol_res = '2' if cifti_output == '91k' else '1'
-        spaces.add(Reference('MNI152NLin6Asym', {'res': vol_res}))
+            # 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