Bug ct duplicate (#22)

* rig_only ct to t1

* head erode skin 9 (18 was too long and required for specific indiv only)

Dockerfile_testpypi

@@ -46,8 +46,9 @@ RUN pip3 install xvfbwrapper \
     pbr \
     nibabel==3.2.2 \
     packaging \
-    pytest \
-    install \
+    pytest
+
+RUN pip3 install install \
     graphviz \
     pybids \
     nipype \

skullTo3d/_version.py

@@ -1,2 +1 @@
-
 __version__ = '0.0.3'

skullTo3d/pipelines/skull_pipe.py

@@ -374,6 +374,8 @@ def create_skull_ct_pipe(name="skull_ct_pipe", params={}):
     align_ct_on_T1 = pe.Node(interface=RegAladin(),
                              name="align_ct_on_T1")
 
+    align_ct_on_T1.inputs.rig_only_flag = True
+
     skull_ct_pipe.connect(inputnode, 'ct',
                           align_ct_on_T1, "flo_file")
 
@@ -411,7 +413,7 @@ def create_skull_ct_pipe(name="skull_ct_pipe", params={}):
             inputnode, ("indiv_params", parse_key, "ct_skull_mask_thr"),
             ct_skull_mask_thr, "indiv_params")
 
-        skull_ct_pipe.connect(align_ct_on_stereo_T1, "out_file",
+        skull_ct_pipe.connect(align_ct_on_stereo_T1, 'out_file',
                               ct_skull_mask_thr, "in_file")
     else:
 
@@ -426,7 +428,7 @@ def create_skull_ct_pipe(name="skull_ct_pipe", params={}):
                 params=parse_key(params, "ct_skull_auto_mask"),
                 name="ct_skull_auto_mask")
 
-        skull_ct_pipe.connect(align_ct_on_stereo_T1, "out_file",
+        skull_ct_pipe.connect(align_ct_on_stereo_T1, 'out_file',
                               ct_skull_auto_mask, "img_file")
 
         skull_ct_pipe.connect(
@@ -849,7 +851,6 @@ def create_skull_petra_pipe(name="skull_petra_pipe", params={}):
     if "petra_skull_fov" in params.keys():
 
         # petra_skull_fov ####### [okey][json]
-
         petra_skull_fov = NodeParams(
             interface=RobustFOV(),
             params=parse_key(params, "petra_skull_fov"),

workflows/params_segment_macaque_ants_skull.json

@@ -157,7 +157,7 @@
         "t1_head_erode_skin":
         {
             "kernel_shape": "boxv",
-            "kernel_size": 18.0
+            "kernel_size": 9.0
         },
         "t1_skull_dilate":
         {
@@ -179,11 +179,11 @@
     {
         "ct_skull_auto_mask":
         {
-            "kmeans": false,
+            "kmeans": true,
             "sample_bins": 30,
             "distance": 10,
-            "operation": "higher",
-            "index": 3
+            "operation": "lower",
+            "index": 2
         },
         "ct_skull_dilate":
         {

workflows/segment_petra.py

@@ -839,7 +839,7 @@ def create_main_workflow(data_dir, process_dir, soft, species, subjects,
                     datasink, '@t1_native_skull_mask')
 
         if "ct" in skull_dt and "skull_ct_pipe" in params.keys():
-            print("rename ct skull pipe")
+            print("rename ct skull pipe 1")
 
             rename_all_skull_ct_derivatives(
                 params, main_workflow, segment_brain_pipe, skull_ct_pipe,