Merge branch 'enh/skip_native'

nipreps · Dec 7, 2016 · e15da51 · e15da51
2 parents 60e98d0 + 15c539c
commit e15da51
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Showing 4 changed files with 23 additions and 13 deletions.
diff --git a/fmriprep/run_workflow.py b/fmriprep/run_workflow.py
@@ -58,6 +58,9 @@ def main():
     g_input.add_argument('-t', '--workflow-type', default='auto', required=False,
                          action='store', choices=['auto', 'ds005', 'ds054'],
                          help='specify workflow type manually')
+    g_input.add_argument('--skip-native', action='store_true',
+                         default=False,
+                         help="don't output timeseries in native space")
 
     #  ANTs options
     g_ants = parser.add_argument_group('specific settings for ANTs registrations')
@@ -92,7 +95,8 @@ def create_workflow(opts):
         'skull_strip_ants': opts.skull_strip_ants,
         'output_dir': op.abspath(opts.output_dir),
         'work_dir': op.abspath(opts.work_dir),
-        'workflow_type': opts.workflow_type
+        'workflow_type': opts.workflow_type,
+        'skip_native': opts.skip_native
     }
 
     # set up logger

diff --git a/fmriprep/workflows/epi.py b/fmriprep/workflows/epi.py
@@ -75,13 +75,6 @@ def epi_hmc(name='EPI_HMC', settings=None):
                                ('out_file', 'epi_mean')]),
     ])
 
-    # Write corrected file in the designated output dir
-    ds_hmc = pe.Node(
-        DerivativesDataSink(base_directory=settings['output_dir'],
-                            suffix='preproc'),
-        name='DerivativesHMC'
-    )
-
     ds_mask = pe.Node(
         DerivativesDataSink(base_directory=settings['output_dir'],
                             suffix='brainmask'),
@@ -111,11 +104,9 @@ def epi_hmc(name='EPI_HMC', settings=None):
     )
 
     workflow.connect([
-        (inputnode, ds_hmc, [('epi', 'source_file')]),
         (inputnode, ds_report, [('epi', 'source_file')]),
         (inputnode, ds_mask, [('epi', 'source_file')]),
         (inputnode, mean_epi_overlay_ds, [('epi', 'origin_file')]),
-        (hmc, ds_hmc, [('out_file', 'in_file')]),
         (bet_hmc, ds_mask, [('mask_file', 'in_file')]),
         (hmc, mean_epi_stripped_overlay, [('mean_img', 'overlay_file')]),
         (bet_hmc, mean_epi_stripped_overlay, [('mask_file', 'in_file')]),
@@ -126,6 +117,18 @@ def epi_hmc(name='EPI_HMC', settings=None):
         (bet_hmc, ds_report, [('out_report', 'in_file')])
     ])
 
+    if not settings["skip_native"]:
+        # Write corrected file in the designated output dir
+        ds_hmc = pe.Node(
+            DerivativesDataSink(base_directory=settings['output_dir'],
+                                suffix='preproc'),
+            name='DerivativesHMC'
+        )
+        workflow.connect([
+            (inputnode, ds_hmc, [('epi', 'source_file')]),
+            (hmc, ds_hmc, [('out_file', 'in_file')])
+        ])
+
     return workflow
 
 

diff --git a/test/workflows/test_base.py b/test/workflows/test_base.py
@@ -11,7 +11,8 @@ def test_wf_ds054_type(self, _):
         # set up
         mock_subject_data = {'t1w': ['um'], 'sbref': ['um'], 'func': 'um'}
         mock_settings = {'output_dir': '.', 'work_dir': '.',
-                         'ants_nthreads': 1, 'biggest_epi_file_size_gb': 1}
+                         'ants_nthreads': 1, 'biggest_epi_file_size_gb': 1,
+                         'skip_native': False}
 
         # run
         wf054 = wf_ds054_type(mock_subject_data, mock_settings)
@@ -39,7 +40,8 @@ def test_wf_ds005_type(self, _):
         # set up
         mock_subject_data = {'func': ''}
         mock_settings = {'output_dir': '.', 'ants_nthreads': 1,
-                         'biggest_epi_file_size_gb': 1}
+                         'biggest_epi_file_size_gb': 1,
+                         'skip_native': False}
 
         # run
         wf005 = wf_ds005_type(mock_subject_data, mock_settings)

diff --git a/test/workflows/test_confounds.py b/test/workflows/test_confounds.py
@@ -17,7 +17,8 @@ class TestConfounds(TestWorkflow):
 
     def test_discover_wf(self):
         # run
-        workflow = discover_wf(stub.settings({'biggest_epi_file_size_gb': 1}))
+        workflow = discover_wf(stub.settings({'biggest_epi_file_size_gb': 1,
+                                              'skip_native': False}))
         workflow.write_hierarchical_dotfile()
 
         # assert