using afni.Automask instead of MaskTool

Author: birajstha

CPAC/func_preproc/func_motion.py

@@ -88,18 +88,20 @@ def calc_motion_stats(wf, cfg, strat_pool, pipe_num, opt=None):
         "inputspec.motion_correct",
     )
 
-    try:
+    if strat_pool.check_rpool("space-bold_desc-brain_mask"):
         wf.connect(
             *strat_pool.get_data("space-bold_desc-brain_mask"),
             gen_motion_stats,
             "inputspec.mask",
         )
-    except:
-        mask_bold = pe.Node(interface=afni.MaskTool(), name=f"mask_bold_{pipe_num}")
-        mask_bold.inputs.outputtype = "NIFTI_GZ"
+    else:
+        automask = pe.Node(interface=afni.Automask(), name=f"automask_bold_{pipe_num}")
+        automask.inputs.dilate = 1
+        automask.inputs.outputtype = "NIFTI_GZ"
+
         node, out = strat_pool.get_data("desc-preproc_bold")
-        wf.connect(node, out, mask_bold, "in_file")
-        wf.connect(mask_bold, "out_file", gen_motion_stats, "inputspec.mask")
+        wf.connect(node, out, automask, "in_file")
+        wf.connect(automask, "out_file", gen_motion_stats, "inputspec.mask")
 
     wf.connect(
         *strat_pool.get_data("desc-movementParameters_motion"),