sketch confounds metadata sink

Author: rciric

fmriprep/workflows/bold/base.py

@@ -360,7 +360,7 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
                 'bold_mni', 'bold_mni_ref' 'bold_mask_mni', 'bold_aseg_mni', 'bold_aparc_mni',
                 'bold_cifti', 'cifti_variant', 'cifti_variant_key', 'confounds', 'surfaces',
                 'aroma_noise_ics', 'melodic_mix', 'nonaggr_denoised_file',
-                'tcompcor_metadata', 'acompcor_metadata']),
+                'confounds_metadata']),
         name='outputnode')
 
     # BOLD buffer: an identity used as a pointer to either the original BOLD
@@ -403,8 +403,7 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
             ('bold_cifti', 'inputnode.bold_cifti'),
             ('cifti_variant', 'inputnode.cifti_variant'),
             ('cifti_variant_key', 'inputnode.cifti_variant_key'),
-            ('tcompcor_metadata', 'inputnode.tcompcor_metadata'),
-            ('acompcor_metadata', 'inputnode.acompcor_metadata')
+            ('confounds_metadata', 'inputnode.confounds_metadata'),
         ]),
     ])
 
@@ -595,10 +594,7 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
             ('outputnode.confounds_file', 'confounds'),
         ]),
         (bold_confounds_wf, outputnode, [
-            ('outputnode.acompcor_metadata', 'acompcor_metadata'),
-        ]),
-        (bold_confounds_wf, outputnode, [
-            ('outputnode.tcompcor_metadata', 'tcompcor_metadata'),
+            ('outputnode.confounds_metadata', 'confounds_metadata'),
         ]),
         # Connect bold_bold_trans_wf
         (bold_split, bold_bold_trans_wf, [
@@ -885,28 +881,17 @@ def init_func_derivatives_wf(output_dir, output_spaces, template, freesurfer,
                     'bold_aparc_mni', 'cifti_variant_key',
                     'confounds', 'surfaces', 'aroma_noise_ics', 'melodic_mix',
                     'nonaggr_denoised_file', 'bold_cifti', 'cifti_variant',
-                    'tcompcor_metadata', 'acompcor_metadata']),
+                    'confounds_metadata']),
         name='inputnode')
 
     ds_confounds = pe.Node(DerivativesDataSink(
         base_directory=output_dir, desc='confounds', suffix='regressors'),
         name="ds_confounds", run_without_submitting=True,
         mem_gb=DEFAULT_MEMORY_MIN_GB)
-    ds_tcc_metadata = pe.Node(DerivativesDataSink(
-        base_directory=output_dir, desc='tcompcor', suffix='decomposition'),
-        name="ds_tcc_metadata", run_without_submitting=True,
-        mem_gb=DEFAULT_MEMORY_MIN_GB)
-    ds_acc_metadata = pe.Node(DerivativesDataSink(
-        base_directory=output_dir, desc='acompcor', suffix='decomposition'),
-        name="ds_acc_metadata", run_without_submitting=True,
-        mem_gb=DEFAULT_MEMORY_MIN_GB)
     workflow.connect([
         (inputnode, ds_confounds, [('source_file', 'source_file'),
-                                   ('confounds', 'in_file')]),
-        (inputnode, ds_tcc_metadata, [('source_file', 'source_file'),
-                                      ('tcompcor_metadata', 'in_file')]),
-        (inputnode, ds_acc_metadata, [('source_file', 'source_file'),
-                                      ('acompcor_metadata', 'in_file')]),
+                                   ('confounds', 'in_file'),
+                                   ('confounds_metadata', 'meta_dict')]),
     ])
 
     # Resample to T1w space

fmriprep/workflows/bold/confounds.py

@@ -28,7 +28,7 @@
 )
 from niworkflows.interfaces.segmentation import ICA_AROMARPT
 from niworkflows.interfaces.utils import (
-    TPM2ROI, AddTPMs, AddTSVHeader, TSV2JSON
+    TPM2ROI, AddTPMs, AddTSVHeader, TSV2JSON, DictMerge
 )
 
 from ...interfaces import (
@@ -127,6 +127,8 @@ def init_bold_confs_wf(mem_gb, metadata, return_all_components=False,
         rois_report
             Reportlet visualizing white-matter/CSF mask used for aCompCor,
             the ROI for tCompCor and the BOLD brain mask.
+        confounds_metadata
+            Confounds metadata dictionary.
 
     """
     workflow = Workflow(name=name)
@@ -166,7 +168,7 @@ def init_bold_confs_wf(mem_gb, metadata, return_all_components=False,
                 't1_mask', 't1_tpms', 't1_bold_xform']),
         name='inputnode')
     outputnode = pe.Node(niu.IdentityInterface(
-        fields=['confounds_file', 'tcompcor_metadata', 'acompcor_metadata']),
+        fields=['confounds_file', 'confounds_metadata']),
         name='outputnode')
 
     # Get masks ready in T1w space
@@ -250,13 +252,17 @@ def init_bold_confs_wf(mem_gb, metadata, return_all_components=False,
 
     # CompCor metadata
     tcc_metadata_fmt = pe.Node(
-        TSV2JSON(index_column='component', drop_columns=['mask'],
+        TSV2JSON(index_column='component', drop_columns=['mask'], output=None,
                  additional_metadata={'Method': 'tCompCor'}, enforce_case=True),
         name='tcc_metadata_fmt')
     acc_metadata_fmt = pe.Node(
-        TSV2JSON(index_column='component',
+        TSV2JSON(index_column='component', output=None,
                  additional_metadata={'Method': 'aCompCor'}, enforce_case=True),
         name='acc_metadata_fmt')
+    mrg_conf_metadata = pe.Node(niu.Merge(2), name='merge_confound_metadata',
+                                run_without_submitting=True)
+    mrg_conf_metadata2 = pe.Node(DictMerge(), name='merge_confound_metadata2',
+                                 run_without_submitting=True)
 
     # Expand model to include derivatives and quadratics
     model_expand = pe.Node(ExpandModel(
@@ -378,15 +384,17 @@ def _pick_wm(files):
         # Confounds metadata
         (tcompcor, tcc_metadata_fmt, [('metadata_file', 'in_file')]),
         (acompcor, acc_metadata_fmt, [('metadata_file', 'in_file')]),
+        (tcc_metadata_fmt, mrg_conf_metadata, [('output', 'in1')]),
+        (acc_metadata_fmt, mrg_conf_metadata, [('output', 'in2')]),
+        (mrg_conf_metadata, mrg_conf_metadata2, [('out', 'in_dicts')]),
 
         # Expand the model with derivatives, quadratics, and spikes
         (concat, model_expand, [('confounds_file', 'confounds_file')]),
         (model_expand, spike_regress, [('confounds_file', 'confounds_file')]),
 
         # Set outputs
         (spike_regress, outputnode, [('confounds_file', 'confounds_file')]),
-        (tcc_metadata_fmt, outputnode, [('out_file', 'tcompcor_metadata')]),
-        (acc_metadata_fmt, outputnode, [('out_file', 'acompcor_metadata')]),
+        (mrg_conf_metadata2, outputnode, [('out_dict', 'confounds_metadata')]),
         (inputnode, rois_plot, [('bold', 'in_file'),
                                 ('bold_mask', 'in_mask')]),
         (tcompcor, mrg_compcor, [('high_variance_masks', 'in1')]),