adding the template_space_func_masking nodeblock

Author: birajstha

CPAC/func_preproc/func_preproc.py

@@ -1611,7 +1611,7 @@ def bold_mask_anatomical_resampled(wf, cfg, strat_pool, pipe_num, opt=None):
 
     Adapted from `DCAN Lab's BOLD mask method from the ABCD pipeline <https://github.com/DCAN-Labs/DCAN-HCP/blob/1d90814/fMRIVolume/scripts/OneStepResampling.sh#L121-L132>`_.
     """
-    anat_brain_to_func_res = anat_brain_to_bold_res(wf, cfg, pipe_num)
+    anat_brain_to_func_res = anat_brain_to_bold_res(wf_name="anat_brain_to_bold_res", cfg, pipe_num)
 
     node, out = strat_pool.get_data("space-template_desc-preproc_T1w")
     wf.connect(
@@ -1836,6 +1836,52 @@ def bold_masking(wf, cfg, strat_pool, pipe_num, opt=None):
 
     return (wf, outputs)
 
+@nodeblock(
+    name="template_space_bold_masking",
+    switch=[
+        ["functional_preproc", "run"],
+        ["functional_preproc", "template_space_func_masking", "run"],
+        ["functional_preproc", "template_space_func_masking", "apply_func_mask_in_template_space"],
+    ],
+    inputs=[("space-template_desc-preproc_bold", "space-template_desc-bold_mask")],
+    outputs={
+        "space-template_desc-preproc_bold": {
+            "Description": "The skull-stripped BOLD time-series.",
+            "SkullStripped": True,
+        },
+        "space-template_desc-brain_bold": {
+            "Description": "The skull-stripped BOLD time-series.",
+            "SkullStripped": True,
+        },
+        "space-template_desc-head_bold": {
+            "Description": "The non skull-stripped BOLD time-series.",
+            "SkullStripped": False,
+        },
+    },
+)
+def template_space_bold_masking(wf, cfg, strat_pool, pipe_num, opt=None):
+    """Mask the bold in template space."""
+    func_edge_detect = pe.Node(
+        interface=afni_utils.Calc(), name=f"template_space_func_extract_brain_{pipe_num}"
+    )
+
+    func_edge_detect.inputs.expr = "a*b"
+    func_edge_detect.inputs.outputtype = "NIFTI_GZ"
+
+    node_head_bold, out_head_bold = strat_pool.get_data("space-template_desc-preproc_bold")
+    wf.connect(node_head_bold, out_head_bold, func_edge_detect, "in_file_a")
+
+    node, out = strat_pool.get_data("space-template_desc-bold_mask")
+    wf.connect(node, out, func_edge_detect, "in_file_b")
+
+    outputs = {
+        "space-template_desc-preproc_bold": (func_edge_detect, "out_file"),
+        "space-template_desc-brain_bold": (func_edge_detect, "out_file"),
+        "space-template_desc-head_bold": (node_head_bold, out_head_bold),
+    }
+
+    return (wf, outputs)
+
 
 @nodeblock(
     name="func_mean",

CPAC/pipeline/cpac_pipeline.py

@@ -1275,7 +1275,6 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None):
                     bold_mask_fsl_afni,
                     bold_mask_anatomical_refined,
                     bold_mask_anatomical_based,
-                    bold_mask_anatomical_resampled,
                     bold_mask_ccs,
                 ],
                 bold_masking,
@@ -1402,6 +1401,13 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None):
         if cfg.voxel_mirrored_homotopic_connectivity["run"]:
             pipeline_blocks += [create_func_to_T1template_symmetric_xfm]
 
+    # Template space functional masking
+    if cfg.functional_preproc["template_space_func_masking"]["run"]:
+        if not rpool.check_rpool("space-template_desc-bold_mask"):
+            pipeline_blocks += bold_mask_anatomical_resampled,
+        if cfg.functional_preproc["template_space_func_masking"]["apply_func_mask_in_template_space"]:
+            pipeline_blocks += apply_func_mask_to_template,
+
     # Nuisance Correction
     generate_only = (
         True not in cfg["nuisance_corrections", "2-nuisance_regression", "run"]