[skip ci] update documentation to reflect new confounds options

Author: rciric

docs/outputs.rst

@@ -173,7 +173,7 @@ motion-correction parameters estimated by fMRIPrep;
 if present, ``non_steady_state_outlier_XX`` columns indicate non-steady state volumes with a single
 ``1`` value and ``0`` elsewhere (*i.e.*, there is one ``non_steady_state_outlier_XX`` column per
 outlier/volume);
-six noise components are calculated using :abbr:`CompCor (Component Based Noise Correction)`, 
+additional noise components are calculated using :abbr:`CompCor (Component Based Noise Correction)`,
 according to both the anatomical (``a_comp_cor_XX``) and temporal (``t_comp_cor_XX``) variants;
 and the motion-related components identified by
 :abbr:`ICA (independent components analysis)`-:abbr:`AROMA (Automatic Removal Of Motion Artifacts)`

docs/workflows.rst

@@ -52,6 +52,9 @@ is presented below:
         use_aroma=False,
         aroma_melodic_dim=-200,
         ignore_aroma_err=False,
+        return_all_components=False,
+        fd_spike_thr=0.5,
+        dv_spike_thr=1.5
     )
 
 
@@ -274,6 +277,9 @@ BOLD preprocessing
         use_aroma=False,
         aroma_melodic_dim=-200,
         ignore_aroma_err=False,
+        return_all_components=False,
+        fd_spike_thr=0.5,
+        dv_spike_thr=1.5
     )
 
 Preprocessing of :abbr:`BOLD (blood-oxygen level-dependent)` files is
@@ -518,7 +524,10 @@ Confounds estimation
         name="discover_wf",
         mem_gb=1,
         metadata={"RepetitionTime": 2.0,
-                  "SliceTiming": [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9]})
+                  "SliceTiming": [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9]},
+        return_all_components=False,
+        fd_spike_thr=0.5,
+        dv_spike_thr=1.5)
 
 Given a motion-corrected fMRI, a brain mask, ``mcflirt`` movement parameters and a
 segmentation, the `discover_wf` sub-workflow calculates potential

fmriprep/workflows/base.py

@@ -87,6 +87,9 @@ def init_fmriprep_wf(subject_list, task_id, echo_idx, run_uuid, work_dir, output
                               use_aroma=False,
                               ignore_aroma_err=False,
                               aroma_melodic_dim=-200,
+                              return_all_components=False,
+                              fd_spike_thr=0.5,
+                              dv_spike_thr=1.5,
                               template_out_grid='native')
 
 
@@ -296,7 +299,10 @@ def init_single_subject_wf(subject_id, task_id, echo_idx, name, reportlets_dir,
                                     template_out_grid='native',
                                     use_aroma=False,
                                     aroma_melodic_dim=-200,
-                                    ignore_aroma_err=False)
+                                    ignore_aroma_err=False,
+                                    return_all_components=False,
+                                    fd_spike_thr=0.5,
+                                    dv_spike_thr=1.5)
 
     Parameters
 

fmriprep/workflows/bold/base.py

@@ -86,6 +86,9 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
                                   use_aroma=False,
                                   ignore_aroma_err=False,
                                   aroma_melodic_dim=-200,
+                                  return_all_components=False,
+                                  fd_spike_thr=0.5,
+                                  dv_spike_thr=1.5,
                                   num_bold=1)
 
     **Parameters**

fmriprep/workflows/bold/confounds.py

@@ -76,7 +76,10 @@ def init_bold_confs_wf(mem_gb, metadata, return_all_components=False,
         from fmriprep.workflows.bold.confounds import init_bold_confs_wf
         wf = init_bold_confs_wf(
             mem_gb=1,
-            metadata={})
+            metadata={},
+            return_all_components=False,
+            fd_spike_thr=0.5,
+            dv_spike_thr=1.5)
 
     **Parameters**