Add gre multiecho (#65)

* create_skull_megre_pipe

* fullskullmask 

* desc-braincrop instead of restrain

* mesh_fullskull_restrain.inputs.KPB = 0.0001
mesh_fullskull_restrain.inputs.NITER = 1000

Author: davidmeunier79

.github/workflows/check_on_PR.yml

@@ -105,11 +105,15 @@ jobs:
 
             python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results -soft ANTS_test_skull -species marmo -sub Tresor -ses 01 -brain_dt T1 T2 -skull_dt T1 petra CT -deriv -pad
 
+            python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results -soft ANTS_test_skullnoisypetra -species marmo -sub Tresor -ses 01 -brain_dt T1 T2 -skull_dt T1 petra CT -deriv -pad
+
             python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results -soft SPM_native_test_skull -species marmo -sub Tresor -ses 01 -brain_dt T1 T2 -skull_dt T1 petra CT -deriv -pad
 
       - name: Running all test pipelines (marmo T2)
         run: |
 
+            python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results -soft ANTS_4animal_test_skull -species marmoT2 -sub Tresor -ses 01 -brain_dt T1 T2 -skull_dt T1 petra CT -deriv -pad
+
             python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results -soft ANTS_test_skull -species marmoT2 -sub Tresor -ses 01 -brain_dt T1 T2 -skull_dt T1 petra CT -deriv -pad
 
             python workflows/segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results -soft SPM_native_test_skull -species marmoT2 -sub Tresor -ses 01 -brain_dt T1 T2 -skull_dt T1 petra CT -deriv -pad