Modif marmo ants skull (#34)

* removed_crop_z_T1, head mesh, copy_header = false for pad + minimal_reg by default, cmd and version in real params
Macatools · Feb 20, 2025 · f371932 · f371932
1 parent f6b4aaf
commit f371932
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Showing 5 changed files with 36 additions and 38 deletions.
diff --git a/workflows/params_segment_macaque_ants_skull.json b/workflows/params_segment_macaque_ants_skull.json
@@ -15,7 +15,7 @@
     	},
         "pad_template":
         {
-            "copy_header" : true,
+            "copy_header" : false,
             "operation" : "PadImage",
             "op2" : "70"
         }

diff --git a/workflows/params_segment_macaque_spm_skull.json b/workflows/params_segment_macaque_spm_skull.json
@@ -6,24 +6,18 @@
     },
     "short_preparation_pipe":
     {
-
         "aladin_T2_on_T1":{},
     	"crop_aladin_pipe":
     	{
-            "pre_crop_z_T1":
-            {
-                "brainsize": 70
-            },
             "reg_T1_on_template":
             {
-            },
-            "reg_T1_on_template2":
-            {
             }
-        },
-        "resample_T1_pad":
+    	},
+        "pad_template":
         {
-            "pad_val": 30
+            "copy_header" : false,
+            "operation" : "PadImage",
+            "op2" : "70"
         }
     },
     "debias":

diff --git a/workflows/params_segment_marmo_ants_skull.json b/workflows/params_segment_marmo_ants_skull.json
@@ -6,36 +6,23 @@
     },
      "short_preparation_pipe":
     {
-        "aladin_T2_on_T1":{},
-
         "use_T2":{},
+        "aladin_T2_on_T1": {},
+
         "crop_aladin_pipe":
         {
             "remove_capsule_pipe":{},
 
             "reg_T1_on_template":
             {
-                "nac_flag": true,
-                "rig_only_flag": true,
-                "nosym_flag": true,
-                "ln_val": 12,
-                "lp_val": 10,
-                "smoo_r_val": 1.0
-            },
-            "reg_T1_on_template2":
-            {
-                "rig_only_flag": true,
-                "nosym_flag": true,
-                "ln_val": 17,
-                "lp_val": 15,
-                "smoo_r_val": 1.0
+                "rig_only_flag": true
             }
     	},
         "pad_template":
         {
-            "copy_header" : true,
+            "copy_header" : false,
             "operation" : "PadImage",
-            "op2" : "70"
+            "op2" : "90"
         }
     },
     "fast":

diff --git a/workflows/params_segment_marmo_spm_skull.json b/workflows/params_segment_marmo_spm_skull.json
@@ -4,19 +4,25 @@
          "template_name": "MBM_v3.0.1",
          "template_stereo_name": "bma-1_0p2mm"
     },
-    "short_preparation_pipe":
+     "short_preparation_pipe":
     {
+        "use_T2":{},
+        "aladin_T2_on_T1": {},
+
         "crop_aladin_pipe":
         {
-            "use_T2": {},
+            "remove_capsule_pipe":{},
+
             "reg_T1_on_template":
             {
-            },
-            "reg_T1_on_template2":
-            {
             }
-        },
-        "resample_T1_pad": {}
+    	},
+        "pad_template":
+        {
+            "copy_header" : false,
+            "operation" : "PadImage",
+            "op2" : "90"
+        }
     },
     "debias":
     {

diff --git a/workflows/segment_skull.py b/workflows/segment_skull.py
@@ -44,6 +44,8 @@
 #           Julien Sein ([email protected])
 #           Adam Sghari ([email protected])
 
+import sys
+
 import os
 import os.path as op
 
@@ -92,11 +94,12 @@
     rename_all_skull_t1_derivatives,
     rename_all_skull_ct_derivatives, rename_all_angio_derivatives)
 
+from skullTo3d._version import __version__
 
 fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
 ##########################################################################
 
-def create_main_workflow(data_dir, process_dir, soft, species, subjects,
+def create_main_workflow(cmd, data_dir, process_dir, soft, species, subjects,
                          sessions, brain_dt, skull_dt, acquisitions,
                          reconstructions, params_file, indiv_params_file,
                          mask_file, template_path, template_files, nprocs,
@@ -880,6 +883,11 @@ def create_main_workflow(data_dir, process_dir, soft, species, subjects,
     main_workflow.write_graph(graph2use="colored")
     main_workflow.config['execution'] = {'remove_unnecessary_outputs': 'false'}
 
+    # saving real params.json
+    params["skullTo3d"] = __version__
+
+    params["full_command"] = cmd
+
     # saving real params.json
     real_params_file = op.join(process_dir, wf_name, "real_params.json")
     with open(real_params_file, 'w+') as fp:
@@ -984,9 +992,12 @@ def main():
 
     args = parser.parse_args()
 
+    cmd = " ".join(sys.argv)
+
     # main_workflow
     print("Initialising the pipeline...")
     create_main_workflow(
+        cmd=cmd,
         data_dir=args.data,
         soft=args.soft,
         process_dir=args.out,