diff --git a/smriprep/cli/utils.py b/smriprep/cli/utils.py
index 2b0a0c6cf2..c624b17d90 100644
--- a/smriprep/cli/utils.py
+++ b/smriprep/cli/utils.py
@@ -38,12 +38,6 @@ def output_space(value):
     """Parse one element of ``--output-spaces``."""
     tpl_args = value.split(':')
     template = tpl_args[0]
-    spaces = []
-    for modifier in tpl_args[1:]:
-        spec = {}
-        mitems = modifier.split('-', 1)
-        spec[mitems[0]] = len(mitems) == 1 or mitems[1]
-        spaces.append((template, spec))
 
     if template in ParseTemplates.EXCEPTIONS or template in LEGACY_SPACES:
         return [(template, {})]
@@ -53,6 +47,14 @@ def output_space(value):
 Template identifier "{}" not found. Please, make sure TemplateFlow is \
 correctly installed and contains the given template identifiers.""".format(template))
 
+    spaces = []
+    for modifiers in tpl_args[1:]:
+        spec = {}
+        for modifier in modifiers.split(','):
+            mitems = modifier.split('-', 1)
+            spec[mitems[0]] = len(mitems) == 1 or mitems[1]
+        spaces.append((template, spec))
+
     if not spaces:
         spaces.append((template, {}))
     return spaces