[FIX] defining SSCNN_MODEL_DIR

neurodocker/templates/freesurfer.yaml

@@ -7,6 +7,9 @@ binaries:
     - version
     optional:
       install_path: /opt/freesurfer-{{ self.version }}
+      license_base64: ""
+      license_path: "/opt"
+      license_file: license.txt
       exclude_paths: |
         average/mult-comp-cor
         lib/cuda
@@ -120,6 +123,8 @@ source:
     optional:
       commit: ""
       license_base64: ""
+      license_path: "/opt"
+      license_file: license.txt
       # The subject dir is not in /opt, like everything else FreeSurfer-related
       # Because if we want to run `neurodocker minify` we want to operate over the `/opt`
       # dir and have the subjects dir excluded
@@ -149,9 +154,6 @@ source:
       source_path: /stage/freesurfer/freesurfer-{{ self.branch }}
       pkg_path: /opt/freesurfer-pkg
       install_path: /opt/freesurfer-{{ self.branch }}
-      # This one has to be quoted with \"s for some reason
-      license_path: "/opt"
-      license_file: license.txt
       cxx_flags: "-msse2 -mfpmath=sse -fPIC -fpermissive"
       c_flags: "-msse2 -mfpmath=sse -fPIC"
       cmake_opts: -DCMAKE_INSTALL_PREFIX={{ self.install_path }} -DBUILD_GUIS={{ self.build_guis }} -DMINIMAL={{ self.minimal }} -DINFANT_MODULE={{ self.infant_module }} -DFS_PACKAGES_DIR={{ self.pkg_path }} -DGFORTRAN_LIBRARIES={{ self.fortran_libs }} -DINSTALL_PYTHON_DEPENDENCIES={{ self.install_python_deps }} -DDISTRIBUTE_FSPYTHON={{ self.distribute_fspython }} -DMARTINOS_BUILD={{ self.martinos_build }} -DGEMS_BUILD_EXECUTABLES={{ self.samseg_atlas_build }} -DCMAKE_CXX_COMPILER=/usr/bin/g++ -DCMAKE_CXX_COMPILER_AR=/usr/bin/ar -DCMAKE_CXX_COMPILER_RANLIB=/usr/bin/ranlib -DCMAKE_CXX_FLAGS="{{ self.cxx_flags }}" -DCMAKE_C_COMPILER=/usr/bin/cc -DCMAKE_C_COMPILER_AR=/usr/bin/ar -DCMAKE_C_COMPILER_RANLIB=/usr/bin/ranlib -DCMAKE_C_FLAGS="{{ self.c_flags }}"
@@ -160,6 +162,7 @@ source:
     FS_LICENSE: "{{ self.license_path }}/{{ self.license_file }}"
     SUBJECTS_DIR: "{{ self.subjects_dir }}"
     FS_INFANT_MODEL: "{{ self.infant_model_dir }}"
+    SSCNN_MODEL_DIR: "{{ self.infant_model_dir }}"/sscnn_skullstrip
     # From https://github.com/freesurfer/freesurfer/blob/54018f7d6f620d6288b28f50e14a0a4ba421757c/Dockerfile#L20-L42
     OS: "Linux"
     PATH: "{{ self.niftyreg_path }}/bin:{{ self.pkg_path }}/mni/current/bin:{{ self.install_path }}/bin:{{ self.install_path }}/fsfast/bin:{{ self.install_path }}/tktools:{{ self.install_path }}/mni/bin:$PATH"