add CLI options for spikes and CompCor

Author: rciric

fmriprep/cli/run.py

@@ -178,6 +178,22 @@ def get_parser():
                          help='Exact or maximum number of MELODIC components to estimate '
                          '(positive = exact, negative = maximum)')
 
+    # Confounds options
+    g_confounds = parser.add_argument_group('Specific options for estimating confounds')
+    g_confounds.add_argument(
+        '--return-all-components', required=False, action='store_true', default=False,
+        help='Include all components estimated in CompCor decomposition in the confounds '
+             'file instead of only the components sufficient to explain 50 percent of '
+             'BOLD variance in each CompCor mask')
+    g.confounds.add_argument(
+        '--fd-spike-threshold', required=False, action='store', default=0.5, type=float,
+        help='Threshold for flagging a frame as an outlier on the basis of framewise '
+             'displacement')
+    g.confounds.add_argument(
+        '--dvars-spike-threshold', required=False, action='store', default=1.5, type=float,
+        help='Threshold for flagging a frame as an outlier on the basis of standardised '
+             'DVARS')
+
     #  ANTs options
     g_ants = parser.add_argument_group('Specific options for ANTs registrations')
     g_ants.add_argument('--skull-strip-template', action='store', default='OASIS',
@@ -747,6 +763,9 @@ def build_workflow(opts, retval):
         use_aroma=opts.use_aroma,
         aroma_melodic_dim=opts.aroma_melodic_dimensionality,
         ignore_aroma_err=opts.ignore_aroma_denoising_errors,
+        return_all_components=opts.return_all_components,
+        fd_spike_thr=opts.fd_spike_threshold,
+        dv_spike_thr=opts.dvars_spike_threshold,
     )
     retval['return_code'] = 0