fix: bug identified by @mgxd on edge --output-spaces cases

Author: oesteban

fmriprep/cli/parser.py

@@ -142,7 +142,7 @@ def _bids_filter(value):
              'option is not enabled, standard EPI-T1 coregistration is performed '
              'using the middle echo.')
     g_conf.add_argument(
-        '--output-spaces', nargs='+', action=OutputReferencesAction, default=SpatialReferences(),
+        '--output-spaces', nargs='*', action=OutputReferencesAction,
         help="""\
 Standard and non-standard spaces to resample anatomical and functional images to. \
 Standard spaces may be specified by the form \
@@ -151,8 +151,8 @@ def _bids_filter(value):
 colon-separated parameters. \
 Non-standard spaces imply specific orientations and sampling grids. \
 Important to note, the ``res-*`` modifier does not define the resolution used for \
-the spatial normalization.
-For further details, please check out \
+the spatial normalization. To generate no BOLD outputs, use this option without specifying \
+any spatial references. For further details, please check out \
 https://fmriprep.readthedocs.io/en/%s/spaces.html""" % (currentv.base_version
                                                         if is_release else 'latest'))
 
@@ -304,12 +304,19 @@ def _bids_filter(value):
 def parse_args(args=None, namespace=None):
     """Parse args and run further checks on the command line."""
     import logging
+    from niworkflows.utils.spaces import Reference, SpatialReferences
     parser = _build_parser()
     opts = parser.parse_args(args, namespace)
     config.execution.log_level = int(max(25 - 5 * opts.verbose_count, logging.DEBUG))
     config.from_dict(vars(opts))
     config.loggers.init()
 
+    # Initialize --output-spaces if not defined
+    if config.execution.output_spaces is None:
+        config.execution.output_spaces = SpatialReferences(
+            [Reference("MNI152NLin2009cAsym", {"res": "native"})]
+        )
+
     # Retrieve logging level
     build_log = config.loggers.cli
 

fmriprep/config.py

@@ -551,22 +551,22 @@ def to_filename(filename):
 def init_spaces(checkpoint=True):
     """Initialize the :attr:`~workflow.spaces` setting."""
     from niworkflows.utils.spaces import Reference, SpatialReferences
-    spaces = execution.output_spaces
+    spaces = execution.output_spaces or SpatialReferences()
     if not isinstance(spaces, SpatialReferences):
         spaces = SpatialReferences(
-            [ref for s in execution.output_spaces.split(' ')
+            [ref for s in spaces.split(' ')
              for ref in Reference.from_string(s)]
         )
 
+    if checkpoint and not spaces.is_cached():
+        spaces.checkpoint()
+
     # Add the default standard space if not already present (required by several sub-workflows)
     if "MNI152NLin2009cAsym" not in spaces.get_spaces(nonstandard=False, dim=(3,)):
         spaces.add(
-            Reference("MNI152NLin2009cAsym", {"res": "native"})
+            Reference("MNI152NLin2009cAsym", {})
         )
 
-    if checkpoint:
-        spaces.checkpoint()
-
     # 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.

fmriprep/tests/test_config.py

@@ -39,3 +39,15 @@ def test_config_spaces():
         format_reference((s.fullname, s.spec))
         for s in spaces.references if s.standard and s.dim == 3
     ]
+
+    config.execution.output_spaces = None
+    config.workflow.use_aroma = False
+    config.init_spaces()
+    spaces = config.workflow.spaces
+
+    assert [str(s) for s in spaces.get_standard(full_spec=True)] == []
+
+    assert [
+        format_reference((s.fullname, s.spec))
+        for s in spaces.references if s.standard and s.dim == 3
+    ] == ['MNI152NLin2009cAsym']