Merge pull request #1983 from mgxd/rf/default-output

FIX: Revert MNI152NLin2009cAsym as default BOLD output

Author: mgxd

fmriprep/cli/run.py

@@ -129,7 +129,7 @@ def get_parser():
              '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, default=SpatialReferences(),
         help="""\
 Standard and non-standard spaces to resample anatomical and functional images to. \
 Standard spaces may be specified by the form \
@@ -138,8 +138,8 @@ def get_parser():
 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'))
 
@@ -718,7 +718,11 @@ def parse_spaces(opts):
 
     """
     spaces = opts.output_spaces
-    spaces.checkpoint()
+    if not spaces.references and not spaces.is_cached():
+        spaces.add('MNI152NLin2009cAsym')
+
+    if not spaces.is_cached():  # spaces may be already checkpointed if users want no BOLD outputs
+        spaces.checkpoint()
 
     if opts.use_aroma:
         # Make sure there's a normalization to FSL for AROMA to use.
@@ -730,15 +734,7 @@ def parse_spaces(opts):
         spaces.add(('fsaverage', {'den': '164k'}))
         spaces.add(('MNI152NLin6Asym', {'res': vol_res}))
 
-    # These arguments implicitly signal expected output
-    if not spaces.references:
-        warnings.warn(
-            "fMRIPrep will not generate preprocessed derivatives because "
-            "none of `--output-spaces`, `--use-aroma`, or `--cifti-output` "
-            "were set."
-        )
-
-    # Add the default standard space (required by several sub-workflows)
+    # 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("MNI152NLin2009cAsym")
     return spaces

setup.cfg

@@ -24,7 +24,7 @@ install_requires =
     nibabel >= 3.0.1
     nipype >=1.3.1
     nitime
-    niworkflows @ git+https://github.com/poldracklab/niworkflows.git@edeea81352f3f2b276f11e42e7829e1c5a03770f
+    niworkflows ~= 1.1.7
     numpy
     pandas
     psutil >=5.4

wrapper/fmriprep_docker.py

@@ -164,8 +164,8 @@ def merge_help(wrapper_help, target_help):
 
     # Make sure we're not clobbering options we don't mean to
     overlap = set(w_flags).intersection(t_flags)
-    expected_overlap = set(['h', 'version', 'w', 'output-spaces',
-                            'fs-license-file', 'fs-subjects-dir', 'use-plugin'])
+    expected_overlap = set(['h', 'version', 'w', 'fs-license-file',
+                            'fs-subjects-dir', 'use-plugin'])
 
     assert overlap == expected_overlap, "Clobbering options: {}".format(
         ', '.join(overlap - expected_overlap))
@@ -249,7 +249,7 @@ def get_parser():
     g_wrap.add_argument('-w', '--work-dir', action='store', type=os.path.abspath,
                         help='path where intermediate results should be stored')
     g_wrap.add_argument(
-        '--output-spaces', nargs="+",
+        '--output-spaces', nargs="*",
         help="""\
 Standard and non-standard spaces to resample anatomical and functional images to. \
 Standard spaces may be specified by the form \