Update deployment and add version notice

.circleci/config.yml

@@ -5,14 +5,12 @@ jobs:
   build:
     machine:
       image: ubuntu-2204:2022.10.2
+    resource_class: large
     parameters:
       version:
         type: string
     steps:
     - checkout
-    - restore_cache:
-        keys:
-        - v_0-image_cache_fs<< parameters.version >>-{{ checksum "Dockerfile_fs<< parameters.version >>" }}
     - run:
         name: load and build
         command: |
@@ -28,11 +26,6 @@ jobs:
           echo "cHJpbnRmICJEeWxhbi5OaWVsc29uQGdtYWlsLmNvbVxuMzcwNjNcbiAqQ1lrZWhQYUNvRDlNXG4gRlM2N1BTWmRFV2lqb1xuIiA+IH4vbGljZW5zZS9saWNlbnNlLnR4dA==" | base64 -d | sh
           cp ~/license/license.txt ~/license_fs<< parameters.version >>/license.txt
           rm -r ~/license
-    - save_cache:
-        key: v_0-image_cache_fs<< parameters.version >>-{{ checksum "Dockerfile_fs<< parameters.version >>" }}-{{ .Revision }}-{{ epoch }}
-        paths:
-        - ~/docker
-        - ~/license_fs<< parameters.version >>
     - persist_to_workspace:
         root: /home/circleci
         paths:
@@ -198,20 +191,31 @@ jobs:
 
               # make sure we have a lowercase repo
               user_name="bids"
-              repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}_fs<< parameters.version >>" | tr '[:upper:]' '[:lower:]')
+              repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
+              FS_MAJOR_VERSION=<< parameters.version >>
+              if [[ FS_MAJOR_VERSION -eq 6 ]]; then
+                FS_VERSION=6.0.1
+              else
+                FS_VERSION=7.4.1
+              fi
 
               if [[ -n "${DOCKER_TOKEN}" ]]; then
                   echo "${DOCKER_TOKEN}" | docker login -u "${DOCKER_USER}" --password-stdin
 
                   : "Pushing to DockerHub ${user_name}/${repo_name}:unstable"
-                  docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:unstable"
-                  docker push "${user_name}/${repo_name}:unstable"
+                  docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:${FS_VERSION}-unstable"
+                  docker push "${user_name}/${repo_name}:${FS_VERSION}-unstable"
+
+                  if [[  -n "${CIRCLE_TAG}" ]]; then
+                      : "Pushing to DockerHub ${user_name}/${repo_name}:${FS_VERSION}-${CIRCLE_TAG}"
+                      if [[ FS_MAJOR_VERSION -eq 6 ]]; then
+                         docker push "${user_name}/${repo_name}:latest"
+                      fi
 
-                  if [[ -n "${CIRCLE_TAG}" ]]; then
-                      : "Pushing to DockerHub ${user_name}/${repo_name}:${CIRCLE_TAG}"
-                      docker push "${user_name}/${repo_name}:latest"
-                      docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:${CIRCLE_TAG}"
-                      docker push "${user_name}/${repo_name}:${CIRCLE_TAG}"
+                      docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:${FS_MAJOR_VERSION}"
+                      docker push ${user_name}/${repo_name}:${FS_MAJOR_VERSION}
+                      docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:${FS_VERSION}-${CIRCLE_TAG}"
+                      docker push "${user_name}/${repo_name}:${FS_VERSION}-${CIRCLE_TAG}"
                   fi
 
               fi
@@ -244,6 +248,7 @@ workflows:
             only: /.*/
 
     - test:
+        name: test_<< matrix.version >>
         matrix:
           parameters:
             version: ['6', '7']
@@ -263,7 +268,7 @@ workflows:
         context:
         - dockerhub
         requires:
-        - test
+        - test_<< matrix.version >>
         filters:
           branches:
             ignore: /.*/

README.md

@@ -2,13 +2,25 @@
 
 ### Description
 This app implements surface reconstruction using Freesurfer. It reconstructs the surface for each subject individually and then
-creates a study specific template. In case there are multiple sessions the Freesurfer longitudinal pipeline is used (creating subject specific templates) unless instructed to combine data across sessions. This app is available for both Freesurfer 6 and 7.
+creates a study specific template. In case there are multiple sessions the Freesurfer longitudinal pipeline is used (creating subject specific templates) unless instructed to combine data across sessions. This app is available for both Freesurfer 6 and 7. 
 
-The current Freesurfer version for Freesurfer 6 is based on: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz
+The current Freesurfer version for Freesurfer 6 is based on: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz  
 The current Freesurfer version for Freesurfer 7 is based on: freesurfer-linux-centos7_x86_64-7.4.1.tar.gz
 
+We only plan to support ove version of Freesurfer 6 and Freesurfer 7 at a time.
+
 The output of the pipeline consist of the SUBJECTS_DIR created during the analysis.
 
+### How to get it
+
+Freesurfer 6 will remain the default image till 2024, at which point Freesurfer 7 will become the default.
+
+You can get the default version with `docker pull bids/freesurfer`.  
+
+Freesurfer 7 is available at `docker pull bids/freesurfer:7`.  
+
+Freesurfer 6 is available at `docker pull bids/freesurfer:6`.  
+
 ### Documentation
  - [Surface reconstruction](https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all)
  - [Study specific template creation](https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates#CreatingaregistrationtemplateinitializedwithFreeSurfertemplate.28DG.29)

run.py

@@ -15,6 +15,7 @@
 def run(command, env={}, ignore_errors=False):
     merged_env = os.environ
     merged_env.update(env)
+
     # DEBUG env triggers freesurfer to produce gigabytes of files
     merged_env.pop('DEBUG', None)
     process = Popen(command, stdout=PIPE, stderr=subprocess.STDOUT, shell=True, env=merged_env)
@@ -27,7 +28,17 @@ def run(command, env={}, ignore_errors=False):
     if process.returncode != 0 and not ignore_errors:
         raise Exception("Non zero return code: %d" % process.returncode)
 
-
+# warn about freesurfer version
+with open(os.path.join(os.environ['FREESURFER_HOME'], 'build-stamp.txt'), 'r') as h:
+    bs = h.read()
+if 'x86_64-7.' in bs:
+    fsversion=7
+else:
+    fsversion=6
+    warn("You are using FreeSurver version 6. "
+        "The FreeSurfer 7 BIDS-App is now available via docker pull bids/freesurfer:v7 . "
+        "FreeSurfer 7 will become the default version in the FreeSurfer BIDS-App begining in 2024. "
+        "From that point on, the FreeSurfer 6 BIDS-App will remain available at bids/freesurfer:v6 .")
 __version__ = open(os.path.join(os.path.dirname(os.path.realpath(__file__)), 'version')).read()
 
 parser = argparse.ArgumentParser(description='FreeSurfer recon-all + custom template generation.')
@@ -519,9 +530,7 @@ def run(command, env={}, ignore_errors=False):
 
     # The call to python2 is only required if we're running Freesurfer 6, we'll need to check version
     # and modify the calls accordingly.
-    with open(os.path.join(os.environ['FREESURFER_HOME'], 'build-stamp.txt'), 'r') as h:
-        bs = h.read()
-    if '-7.' in bs:
+    if fsversion == 7:
         cmd_start = ''
     else:
         cmd_start = 'python2 '