diff --git a/workflows/params_segment_marmo_ants_4animal_skull.json b/workflows/params_segment_marmo_ants_4animal_skull.json index c752c9a..5893ae2 100644 --- a/workflows/params_segment_marmo_ants_4animal_skull.json +++ b/workflows/params_segment_marmo_ants_4animal_skull.json @@ -1,7 +1,7 @@ { "general": { - "template_name": "MBM_v3.0.1_6seg_stereoINT" + "template_name": "template_MBM_space-stereoINTv2" }, "short_preparation_pipe": { @@ -17,14 +17,6 @@ "rig_only_flag":true } }, - "pad_template": - { - "operation" : "PadImage", - "op2" : "90" - }, - "denoise": - { - }, "fast": { "args": "-l 3" @@ -45,16 +37,12 @@ }, "brain_segment_pipe": { - "reg": + "reg_f3d": { - "n": 2, - "m": "ref", - "dof": 12 }, "segment_atropos_pipe": { "use_priors":0.0, - "Atropos": { "dimension": 3 @@ -66,7 +54,9 @@ "wm": 3, "csf": 4 } - } + }, + "parcel_gm": + {} }, "export_5tt_pipe": { diff --git a/workflows/segment_skull.py b/workflows/segment_skull.py index 6762f6a..68cf601 100644 --- a/workflows/segment_skull.py +++ b/workflows/segment_skull.py @@ -376,6 +376,18 @@ def create_main_workflow(cmd, data_dir, process_dir, soft, species, subjects, "Could not find template_seg {}".format(template_seg) params_template["template_seg"] = template_seg + elif len(template_files) == 4: + + template_seg = os.path.join(template_path, template_files[2]) + assert os.path.exists(template_seg), \ + "Could not find template_seg {}".format(template_seg) + params_template["template_seg"] = template_seg + + template_parcel = os.path.join(template_path, template_files[3]) + assert os.path.exists(template_parcel), \ + "Could not find template_parcel {}".format(template_parcel) + params_template["template_parcel"] = template_parcel + elif len(template_files) == 5: template_gm = os.path.join(template_path, template_files[2])