[HOT] Hotfix noskullmask noheadmask (#59)

nohead/noskull in rename ssoft but noheadmask/noskullmask in utils_params
if t1, skull_t1_pipe is empty when noheadmask -> bug , sorted with adding one empty node

Author: davidmeunier79

docs/command.rst

@@ -74,20 +74,33 @@ mandatory parameters
 
   * ``_4animal`` :  will use bet4animal (FSL) for brain extraction, for faster computation (by default atlas_brex is used)
   * ``_quick`` : will use hd-bet (Deep Learning) for brain extraction, for faster computation (by default atlas_brex is used)
-  **NB: ** hd-bet requires a specific version of macapype/skullTo3d, not available by default
+
+  **NB:** hd-bet requires a specific version of macapype/skullTo3d, not available by default
+
+|
 
   This option should be used if the coregistration to template in preparation is not performed correctly:
 
   * ``_robustreg`` (at the end) to have a more robust registration (in two steps)
 
+|
+
   Finally, these option are available (to place after SPM or ANTS) and will modify the parameters but can be launched in sequence:
 
   * ``_test`` : (at the end) to check if the full pipeline is coherent (will only generate the graph.dot and graph.png)
   * ``_prep`` (at the end) will perform data preparation (no brain extraction and segmentation)
   * ``_noseg`` (at the end) will perform data preparation and brain extraction (no segmentation)
 
+|
+
   **Some options are specific to skullTo3d:**
-  *  ``_skull`` after SPM or ANTS if you want to process skull or angio *specific to skullTo3d*; otherwise the main pipelines of macapype will be launched (only brain segmentation will be performed) **NB : ** ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra
+
+  *  ``_skull`` after SPM or ANTS if you want to process skull or angio *specific to skullTo3d*; otherwise the main pipelines of macapype will be launched (only brain segmentation will be performed)
+
+  **NB :** ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra
+
+  **NB :** ``-soft skull`` without processing brain is possible, but is still experimental. It only works if ``-skull_dt CT petra`` and ``-deriv`` and ``-padback`` are NOT defined
+
   * ``_noskullmask`` (at the end) will perform realignement to stereo and headmask (only realignement for CT)
   * ``_noheadmask`` (at the end) will perform only realignement to stereo
 

skullTo3d/nodes/utils.py

@@ -0,0 +1,4 @@
+
+def empty_node(in_file):
+    out_file = in_file
+    return out_file

skullTo3d/pipelines/skull_pipe.py

@@ -31,6 +31,8 @@
 
 from macapype.nodes.correct_bias import itk_debias
 
+from skullTo3d.nodes.utils import empty_node
+
 from skullTo3d.nodes.skull import mask_auto_img
 
 from macapype.nodes.prepare import apply_li_thresh
@@ -510,6 +512,16 @@ def create_skull_t1_pipe(name="skull_t1_pipe", params={}):
         skull_t1_pipe.connect(inputnode, "indiv_params",
                               headmask_t1_pipe, "inputnode.indiv_params")
     else:
+        empty = pe.Node(
+                interface=niu.Function(
+                    input_names=["in_file"],
+                    output_names=["out_file"],
+                    function=empty_node),
+                name="empty")
+
+        skull_t1_pipe.connect(inputnode, "stereo_T1",
+                              empty, "in_file")
+
         return skull_t1_pipe
 
     skull_t1_pipe.connect(

skullTo3d/utils/utils_params.py

@@ -1,5 +1,4 @@
 
-
 def update_skull_params(ssoft, params):
 
     if "noheadmask" in ssoft:

workflows/segment_skull.py

@@ -178,11 +178,11 @@ def create_main_workflow(cmd, data_dir, process_dir, soft, species, subjects,
     if 'prep' in ssoft:
         new_ssoft.remove('prep')
 
-    if 'noskull' in ssoft:
-        new_ssoft.remove('noskull')
+    if 'noskullmask' in ssoft:
+        new_ssoft.remove('noskullmask')
 
-    if 'nohead' in ssoft:
-        new_ssoft.remove('nohead')
+    if 'noheadmask' in ssoft:
+        new_ssoft.remove('noheadmask')
 
     if 'noseg' in ssoft:
         new_ssoft.remove('noseg')