run aCompCor for WM, CSF, and combined masks

Author: rciric

fmriprep/data/boilerplate.bib

@@ -220,7 +220,7 @@ @article{power_fd_dvars
     year = 2014
 }
 
-@article{confounds_satterthwaite_2012,
+@article{confounds_satterthwaite_2013,
     author = {Satterthwaite, Theodore D. and Elliott, Mark A. and Gerraty, Raphael T. and Ruparel, Kosha and Loughead, James and Calkins, Monica E. and Eickhoff, Simon B. and Hakonarson, Hakon and Gur, Ruben C. and Gur, Raquel E. and Wolf, Daniel H.},
     doi = {10.1016/j.neuroimage.2012.08.052},
     issn = {10538119},

fmriprep/workflows/bold/confounds.py

@@ -143,7 +143,7 @@ def init_bold_confs_wf(mem_gb, metadata, name="bold_confs_wf"):
 placed within the corresponding confounds file.
 The confound time series derived from head motion estimates and global
 signals were expanded with the inclusion of temporal derivatives and
-quadratic terms for each [@confounds_satterthwaite_2012].
+quadratic terms for each [@confounds_satterthwaite_2013].
 Frames that exceeded a threshold of 0.2 mm FD or 20 DVARS were classified
 as motion outliers [following @power_fd_dvars].
 """
@@ -190,6 +190,8 @@ def init_bold_confs_wf(mem_gb, metadata, name="bold_confs_wf"):
                     name="fdisp", mem_gb=mem_gb)
 
     # a/t-CompCor
+    mrg_lbl_cc = pe.Node(niu.Merge(3), name='merge_rois_cc', run_without_submitting=True)
+
     tcompcor = pe.Node(
         TCompCor(components_file='tcompcor.tsv', header_prefix='t_comp_cor_', pre_filter='cosine',
                  save_pre_filter=True, num_components='all', save_metadata=True,
@@ -198,7 +200,8 @@ def init_bold_confs_wf(mem_gb, metadata, name="bold_confs_wf"):
 
     acompcor = pe.Node(
         ACompCor(components_file='acompcor.tsv', header_prefix='a_comp_cor_', pre_filter='cosine',
-                 save_pre_filter=True, num_components='all', save_metadata=True),
+                 save_pre_filter=True, num_components='all', save_metadata=True,
+                 mask_names=['combined', 'CSF', 'WM'], merge_method='none'),
         name="acompcor", mem_gb=mem_gb)
 
     # Set TR if present
@@ -325,7 +328,10 @@ def _pick_wm(files):
         (inputnode, acompcor, [('bold', 'realigned_file')]),
         (inputnode, acompcor, [('skip_vols', 'ignore_initial_volumes')]),
         (acc_tfm, acc_msk, [('output_image', 'roi_file')]),
-        (acc_msk, acompcor, [('out', 'mask_files')]),
+        (acc_msk, mrg_lbl_cc, [('out', 'in1')]),
+        (csf_msk, mrg_lbl_cc, [('out', 'in2')]),
+        (wm_msk, mrg_lbl_cc, [('out', 'in3')]),
+        (mrg_lbl_cc, acompcor, [('out', 'mask_files')]),
 
         # Global signals extraction (constrained by anatomy)
         (inputnode, signals, [('bold', 'in_file')]),