Correct baboon3 ants quick (#300)

* forgot atlas_brex in ants quick...

Author: davidmeunier79

Dockerfile_macapype_env

@@ -35,7 +35,9 @@ RUN mkdir /opt/mcr_install \
 # Install SPM Standalone in /opt/spm12/
 ENV SPM_VERSION 12
 ENV SPM_REVISION r7771
-ENV LD_LIBRARY_PATH /opt/mcr/${MCR_VERSION}/runtime/glnxa64:/opt/mcr/${MCR_VERSION}/bin/glnxa64:/opt/mcr/${MCR_VERSION}/sys/os/glnxa64:/opt/mcr/${MCR_VERSION}/sys/opengl/lib/glnxa64:/opt/mcr/${MCR_VERSION}/extern/bin/glnxa64
+
+ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/mcr/${MCR_VERSION}/runtime/glnxa64:/opt/mcr/${MCR_VERSION}/bin/glnxa64:/opt/mcr/${MCR_VERSION}/sys/os/glnxa64:/opt/mcr/${MCR_VERSION}/sys/opengl/lib/glnxa64:/opt/mcr/${MCR_VERSION}/extern/bin/glnxa64
+
 ENV MCR_INHIBIT_CTF_LOCK 1
 ENV SPM_HTML_BROWSER 0
 # Running SPM once with "function exit" tests the succesfull installation *and*

Dockerfile_spm_hdbet

@@ -9,7 +9,7 @@
 #
 # Timestamp: 2020/12/02 18:33:44 UTC
 
-FROM macatools/macapype_env:v0.2.2-spm
+FROM macatools/macapype_env:v0.2.3-spm
 
 USER root
 
@@ -53,7 +53,7 @@ RUN python -m pip install HD-BET
 
 ############################################# install macapype
 
-RUN python -m pip install --pre macapype
+RUN python -m pip install macapype --upgrade
 RUN python -c "import macapype; print(macapype.__version__)"
 
 ################################################## Finishing
@@ -64,3 +64,5 @@ RUN rm -rf \
      /tmp/hsperfdata* \
      /var/*/apt/*/partial \
      /var/log/apt/term*
+
+ENV LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH

macapype/utils/utils_params.py

@@ -129,6 +129,9 @@ def update_params(ssoft=[], subjects=None, sessions=None,
             indiv_params=indiv_params, params=params, extra_wf_name="")
 
     # modifying crop_aladin
+    if "short_preparation_pipe" not in params:
+        return params, indiv_params, extra_wf_name
+
     params_spp = params["short_preparation_pipe"]
 
     if "crop_aladin_pipe" in params_spp.keys():

workflows/params_segment_baboon3_ants_quick.json

@@ -32,14 +32,8 @@
     },
     "extract_pipe":
     {
-        "atlas_brex":
+        "hdbet":
         {
-            "f": 0.7,
-            "reg": 1,
-            "msk": "b,0.5,0,0",
-            "wrp": "10,10,10",
-            "dil": 1,
-            "nrm": 1
 
         }
     },