fix: update the --output-spaces option to be more consistent

with fmriprep 20 and with the objectives of dmriprep.

Author: oesteban

dmriprep/cli/run.py

@@ -33,7 +33,7 @@ def check_deps(workflow):
 
 def get_parser():
     """Build parser object."""
-    from niworkflows.utils.spaces import Reference, SpatialReferences, OutputReferencesAction
+    from niworkflows.utils.spaces import Reference, OutputReferencesAction
     from packaging.version import Version
     from ..__about__ import __version__
     from .version import check_latest, is_flagged
@@ -102,19 +102,21 @@ def get_parser():
         '--longitudinal', action='store_true',
         help='treat dataset as longitudinal - may increase runtime')
     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 \
 ``<SPACE>[:cohort-<label>][:res-<resolution>][...]``, where ``<SPACE>`` is \
 a keyword designating a spatial reference, and may be followed by optional, \
 colon-separated parameters. \
 Non-standard spaces imply specific orientations and sampling grids. \
+The default value of this flag (meaning, if the argument is not include in the command line) \
+is ``--output-spaces orig`` - the original space and sampling grid of the original DWI data. \
 Important to note, the ``res-*`` modifier does not define the resolution used for \
-the spatial normalization. To generate no DWI outputs, use this option without specifying \
-any spatial references. For further details, please check out \
-https://www.nipreps.org/dmriprep/en/%s/spaces.html""" % (currentv.base_version
-                                                         if is_release else 'latest'))
+the spatial normalization. To generate no DWI outputs (if that is intended for some reason), \
+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'))
 
     #  ANTs options
     g_ants = parser.add_argument_group('Specific options for ANTs registrations')
@@ -416,7 +418,11 @@ def build_workflow(opts, retval):
         retval['return_code'] = 1
         return retval
 
-    output_spaces = parse_spaces(opts)
+    # Initialize --output-spaces if not defined
+    output_spaces = opts.output_spaces
+    if opts.output_spaces is None:
+        from niworkflows.utils.spaces import Reference, SpatialReferences
+        output_spaces = SpatialReferences([Reference("orig", {})])
 
     # Set up some instrumental utilities
     run_uuid = '%s_%s' % (strftime('%Y%m%d-%H%M%S'), uuid.uuid4())
@@ -563,23 +569,6 @@ def build_workflow(opts, retval):
     return retval
 
 
-def parse_spaces(opts):
-    """Ensure the spaces are correctly parsed."""
-    from sys import stderr
-    from collections import OrderedDict
-    # Set the default template to 'MNI152NLin2009cAsym'
-    output_spaces = opts.output_spaces or OrderedDict([('MNI152NLin2009cAsym', {})])
-
-    FS_SPACES = set(['fsnative', 'fsaverage', 'fsaverage6', 'fsaverage5'])
-    if opts.run_reconall and not list(FS_SPACES.intersection(output_spaces.keys())):
-        print("""\
-Although ``--fs-no-reconall`` was not set (i.e., FreeSurfer is to be run), no FreeSurfer \
-output space (valid values are: %s) was selected. Adding default "fsaverage5" to the \
-list of output spaces.""" % ', '.join(FS_SPACES), file=stderr)
-        output_spaces['fsaverage5'] = {}
-    return output_spaces
-
-
 if __name__ == '__main__':
     raise RuntimeError("dmriprep/cli/run.py should not be run directly;\n"
                        "Please `pip install` dmriprep and use the `dmriprep` command")