Feature/stereotaxy fct

autoafids/config/snakebids.yml

@@ -143,7 +143,7 @@ parse_args:
 
   --stereotaxy:
     help: 'Predict stereotactic target coordinates from output AFIDs. Also supplies AC-PC transform matrix (4x4) in the process.{STN = subthalamic nucelus, cZI = caudal zona incerta}'
-    choices: ['STN','cZI']
+    choices: ['STN','cZI', 'fct', 'RN']
     default: false
     required: false
 
@@ -236,8 +236,13 @@ resource_urls:
 #Stereotaxy models 
 STN: 'resources/stereotaxy/STN.pkl'
 cZI: 'resources/stereotaxy/cZI.pkl'
+fct: 'resources/stereotaxy/fct.pkl'
+RN: 'resources/stereotaxy/RN.pkl'
+
 template_fcsv: 'resources/stereotaxy/target_template.fcsv'
 cZI_template_fcsv: 'resources/stereotaxy/cZI_target_template.fcsv'
+fct_template_fcsv: 'resources/stereotaxy/fct_target_template.fcsv'
+RN_template_fcsv: 'resources/stereotaxy/RN_target_template.fcsv'
 
 plugins.validator.skip: False
 root: results

autoafids/resources/stereotaxy/RN_target_template.fcsv

@@ -0,0 +1,5 @@
+# Markups fiducial file version = 4.11
+# CoordinateSystem = RAS
+# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID
+1,afid1_x,afid1_y,afid1_z,0,0,0,1,1,1,1,r_RN,Predicted Right RN,vtkMRMLScalarVolumeNode1
+2,afid2_x,afid2_y,afid2_z,0,0,0,1,1,1,1,l_RN,Predicted Left RN,vtkMRMLScalarVolumeNode1

autoafids/resources/stereotaxy/cZI_target_template.fcsv

@@ -1,5 +1,5 @@
 # Markups fiducial file version = 4.11
 # CoordinateSystem = RAS
 # columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID
-1,afid1_x,afid1_y,afid1_z,0,0,0,1,1,1,1,1,Predicted Right cZI ,vtkMRMLScalarVolumeNode1
-2,afid2_x,afid2_y,afid2_z,0,0,0,1,1,1,1,2,Predicted Left cZI,vtkMRMLScalarVolumeNode1
+1,afid1_x,afid1_y,afid1_z,0,0,0,1,1,1,1,r_cZi,Predicted Right cZI ,vtkMRMLScalarVolumeNode1
+2,afid2_x,afid2_y,afid2_z,0,0,0,1,1,1,1,l_cZi,Predicted Left cZI,vtkMRMLScalarVolumeNode1

autoafids/resources/stereotaxy/fct_target_template.fcsv

@@ -0,0 +1,5 @@
+# Markups fiducial file version = 4.11
+# CoordinateSystem = RAS
+# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID
+1,afid1_x,afid1_y,afid1_z,0,0,0,1,1,1,1,r_fct,Predicted Right fct ,vtkMRMLScalarVolumeNode1
+2,afid2_x,afid2_y,afid2_z,0,0,0,1,1,1,1,l_fct,Predicted Left fct,vtkMRMLScalarVolumeNode1

autoafids/resources/stereotaxy/target_template.fcsv

@@ -1,5 +1,5 @@
 # Markups fiducial file version = 4.11
 # CoordinateSystem = RAS
 # columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID
-1,afid1_x,afid1_y,afid1_z,0,0,0,1,1,1,1,1,Predicted Right STN ,vtkMRMLScalarVolumeNode1
-2,afid2_x,afid2_y,afid2_z,0,0,0,1,1,1,1,2,Predicted Left STN,vtkMRMLScalarVolumeNode1
+1,afid1_x,afid1_y,afid1_z,0,0,0,1,1,1,1,r_STN,Predicted Right STN ,vtkMRMLScalarVolumeNode1
+2,afid2_x,afid2_y,afid2_z,0,0,0,1,1,1,1,l_STN,Predicted Left STN,vtkMRMLScalarVolumeNode1

autoafids/workflow/Snakefile

@@ -96,7 +96,7 @@ resolution = float(config["res"])
 
 templatet1w = config["templatet1w"]
 
-if config["stereotaxy"] in ["STN", "cZI"]:
+if config["stereotaxy"] in ["STN", "cZI", "fct", "RN"]:
     stereotaxy_target = config["stereotaxy"]
     print("..... Stereotaxy Target Enabled .....")
     stereotaxy_enabled = True

autoafids/workflow/rules/stereotaxy.smk

@@ -40,15 +40,28 @@ rule stereotaxy:
     params:
         model=str(Path(workflow.basedir).parent / config[stereotaxy_target]),
         midpoint="PMJ",
+        target=stereotaxy_target,
         target_fcsv=str(
             Path(workflow.basedir).parent
             / (
                 config["cZI_template_fcsv"]
                 if stereotaxy_target == "cZI"
-                else config["template_fcsv"]
+                else (
+                    config["fct_template_fcsv"]
+                    if stereotaxy_target == "fct"
+                    else (
+                        config["RN_template_fcsv"]
+                        if stereotaxy_target == "RN"
+                        else config["template_fcsv"]
+                    )
+                )
             )
         ),
     conda:
         "../envs/skimage.yaml"
     script:
-        "../scripts/stereotaxy.py"
+        (
+            "../scripts/16_afid_stereotaxy.py"
+            if stereotaxy_target in ["RN", "fct", "cZI"]
+            else "../scripts/stereotaxy.py"
+        )