More stuff.

src/fmripost_phase/utils/utils.py

@@ -27,6 +27,10 @@ def clean_datasinks(workflow: pe.Workflow) -> pe.Workflow:
     for node in workflow.list_node_names():
         if node.split('.')[-1].startswith('ds_'):
             workflow.get_node(node).interface.out_path_base = ''
+
+        if node.split('.')[-1].startswith('ds_report_'):
+            workflow.get_node(node).interface.datatype = 'figures'
+
     return workflow
 
 

src/fmripost_phase/workflows/base.py

@@ -279,6 +279,7 @@ def init_single_subject_wf(subject_id: str):
 
 def init_single_run_wf(bold_file):
     """Set up a single-run workflow for fMRIPost-Phase."""
+    from fmriprep.utils.bids import dismiss_echo
     from fmriprep.utils.misc import estimate_bold_mem_usage
     from fmriprep.workflows.bold.apply import init_bold_volumetric_resample_wf
     from fmriprep.workflows.bold.stc import init_bold_stc_wf
@@ -291,6 +292,7 @@ def init_single_run_wf(bold_file):
     from fmripost_phase.interfaces.bids import DerivativesDataSink
     from fmripost_phase.interfaces.laynii import LayNiiPhaseJolt
     from fmripost_phase.utils.bids import collect_derivatives, extract_entities
+    from fmripost_phase.workflows.confounds import init_bold_confs_wf
     from fmripost_phase.workflows.regression import init_phase_regression_wf
 
     spaces = config.workflow.spaces
@@ -481,7 +483,30 @@ def init_single_run_wf(bold_file):
         pass
 
     # Compute confounds, including HighCor
-    pass
+    bold_confounds_wf = init_bold_confs_wf(
+        mem_gb=mem_gb['largemem'],
+        metadata=bold_metadata,
+        regressors_all_comps=config.workflow.regressors_all_comps,
+        name='bold_confounds_wf',
+    )
+    # TODO: Set 'phase', 'bold_mask', and 'skip_vols'
+
+    ds_confounds = pe.Node(
+        DerivativesDataSink(
+            desc='confounds',
+            suffix='timeseries',
+            dismiss_entities=dismiss_echo(),
+        ),
+        name='ds_confounds',
+        run_without_submitting=True,
+        mem_gb=config.DEFAULT_MEMORY_MIN_GB,
+    )
+    workflow.connect([
+        (bold_confounds_wf, ds_confounds, [
+            ('outputnode.confounds_file', 'in_file'),
+            ('outputnode.confounds_metadata', 'meta_dict'),
+        ]),
+    ])  # fmt:skip
 
     # Fill-in datasinks seen so far
     for node in workflow.list_node_names():

src/fmripost_phase/workflows/confounds.py

@@ -5,9 +5,6 @@ def init_bold_confs_wf(
     mem_gb: float,
     metadata: dict,
     regressors_all_comps: bool,
-    regressors_dvars_th: float,
-    regressors_fd_th: float,
-    freesurfer: bool = False,
     name: str = 'bold_confs_wf',
 ):
     """Build a workflow to generate and write out confounding signals.
@@ -23,6 +20,8 @@ def init_bold_confs_wf(
     censored and high-pass filtered using a :abbr:`DCT (discrete cosine transform)` basis.
     The cosine basis, as well as one regressor per censored volume, are included
     for convenience.
+
+    XXX: What about tissue time series from the jolt and/or jump files?
     """
     from fmriprep.interfaces.confounds import FilterDropped
     from fmriprep.utils.bids import dismiss_echo
@@ -45,15 +44,9 @@ def init_bold_confs_wf(
     inputnode = pe.Node(
         niu.IdentityInterface(
             fields=[
-                'bold',
                 'phase',
                 'bold_mask',
-                'movpar_file',
-                'rmsd_file',
                 'skip_vols',
-                't1w_mask',
-                't1w_tpms',
-                'boldref2anat_xfm',
             ],
         ),
         name='inputnode',
@@ -63,9 +56,7 @@ def init_bold_confs_wf(
             fields=[
                 'confounds_file',
                 'confounds_metadata',
-                'acompcor_masks',
-                'tcompcor_mask',
-                'crown_mask',
+                'highcor_mask',
             ],
         ),
         name='outputnode',
@@ -160,7 +151,7 @@ def init_bold_confs_wf(
         (highcor, hcc_metadata_filter, [('metadata_file', 'in_file')]),
         (hcc_metadata_filter, hcc_metadata_fmt, [('out_file', 'in_file')]),
         (hcc_metadata_fmt, outputnode, [('output', 'confounds_metadata')]),
-        (highcor, outputnode, [('high_variance_masks', 'tcompcor_mask')]),
+        (highcor, outputnode, [('high_variance_masks', 'highcor_mask')]),
         (highcor, rois_plot, [('high_variance_masks', 'in_rois')]),
         (rois_plot, ds_report_bold_rois, [('out_report', 'in_file')]),
         (highcor, compcor_plot, [('metadata_file', 'in1')]),