ENH: Output compcor masks if --debug compcor passed

Author: effigies

fmriprep/workflows/bold/base.py

@@ -303,6 +303,8 @@ def init_func_preproc_wf(bold_file):
             ('cifti_metadata', 'inputnode.cifti_metadata'),
             ('cifti_density', 'inputnode.cifti_density'),
             ('confounds_metadata', 'inputnode.confounds_metadata'),
+            ('acompcor_masks', 'inputnode.acompcor_masks'),
+            ('tcompcor_mask', 'inputnode.tcompcor_mask'),
         ]),
     ])
 
@@ -496,9 +498,9 @@ def init_func_preproc_wf(bold_file):
             ('outputnode.bold_mask', 'inputnode.bold_mask')]),
         (bold_confounds_wf, outputnode, [
             ('outputnode.confounds_file', 'confounds'),
-        ]),
-        (bold_confounds_wf, outputnode, [
             ('outputnode.confounds_metadata', 'confounds_metadata'),
+            ('outputnode.acompcor_masks', 'acompcor_masks'),
+            ('outputnode.tcompcor_mask', 'tcompcor_mask'),
         ]),
         # Connect bold_bold_trans_wf
         (bold_split, bold_bold_trans_wf, [

fmriprep/workflows/bold/confounds.py

@@ -193,7 +193,7 @@ def init_bold_confs_wf(
                 'skip_vols', 't1w_mask', 't1w_tpms', 't1_bold_xform']),
         name='inputnode')
     outputnode = pe.Node(niu.IdentityInterface(
-        fields=['confounds_file', 'confounds_metadata']),
+        fields=['confounds_file', 'confounds_metadata', 'acompcor_masks', 'tcompcor_mask']),
         name='outputnode')
 
     # DVARS
@@ -392,6 +392,8 @@ def _select_cols(table):
         # Set outputs
         (spike_regress, outputnode, [('confounds_file', 'confounds_file')]),
         (mrg_conf_metadata2, outputnode, [('out_dict', 'confounds_metadata')]),
+        (tcompcor, outputnode, [("high_variance_masks", "tcompcor_mask")]),
+        (acc_msk_bin, outputnode, [("out_file", "acompcor_masks")]),
         (inputnode, rois_plot, [('bold', 'in_file'),
                                 ('bold_mask', 'in_mask')]),
         (tcompcor, mrg_compcor, [('high_variance_masks', 'in1')]),

fmriprep/workflows/bold/outputs.py

@@ -4,8 +4,9 @@
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu
 
-from ...config import DEFAULT_MEMORY_MIN_GB
-from ...interfaces import DerivativesDataSink
+from fmriprep import config
+from fmriprep.config import DEFAULT_MEMORY_MIN_GB
+from fmriprep.interfaces import DerivativesDataSink
 
 
 def init_func_derivatives_wf(
@@ -62,7 +63,7 @@ def init_func_derivatives_wf(
         'bold_mask_native', 'cifti_variant', 'cifti_metadata', 'cifti_density',
         'confounds', 'confounds_metadata', 'melodic_mix', 'nonaggr_denoised_file',
         'source_file', 'surf_files', 'surf_refs', 'template', 'spatial_reference',
-        'bold2anat_xfm', 'anat2bold_xfm']),
+        'bold2anat_xfm', 'anat2bold_xfm', 'acompcor_masks', 'tcompcor_mask']),
         name='inputnode')
 
     raw_sources = pe.Node(niu.Function(function=_bids_relative), name='raw_sources')
@@ -338,6 +339,22 @@ def init_func_derivatives_wf(
                                         (('cifti_metadata', _read_json), 'meta_dict')])
         ])
 
+    if "compcor" in config.execution.debug:
+        ds_acompcor_masks = pe.Node(
+            DerivativesDataSink(
+                base_directory=output_dir, desc=[f"CompCor{_}" for _ in "CWA"], suffix="mask"),
+            name="ds_acompcor_masks", run_without_submitting=True)
+        ds_tcompcor_mask = pe.Node(
+            DerivativesDataSink(
+                base_directory=output_dir, desc="CompCorT", suffix="mask"),
+            name="ds_tcompcor_mask", run_without_submitting=True)
+        workflow.connect([
+            (inputnode, ds_acompcor_masks, [("acompcor_masks", "in_file"),
+                                            ("source_file", "source_file")]),
+            (inputnode, ds_tcompcor_mask, [("tcompcor_mask", "in_file"),
+                                           ("source_file", "source_file")]),
+        ])
+
     return workflow