Installation of fs:fsData and proc:genProcData

Prerequisites:

• install a XNAT instance. Follow https://wiki.xnat.org/display/XNAT16/XNAT+1.6+Installation+Guide to install XNAT

On XNAT VM:

1. Make a BACKUP of your $XNAT_HOME, postgres db, and tomcat deployment
2. Stop tomcat
3. Remove default FreeSurfer files if installed:

[root@xnat-server ~]#rm -r ${XNAT_HOME}/plugin-resources/project-skeletons/xnat/src/schemas/fs
[root@xnat-server ~]#rm -r ${XNAT_HOME}/projects/xnat/src/schemas/fs
[root@xnat-server ~]#rm -r ${XNAT_HOME}/deployments/xnat/src/schemas/fs

You also need to delete FS files from tomcat webapps directory if already deployed.

4. Add modules

[root@xnat-server ~]#cd ${XNAT_HOME}
[root@xnat-server ~]#mkdir modules

Copy the files from dax/xnat_modules/jar_files: fs_module.jar & proc_module.jar _{:sub:~``</sub> [root@xnat-server ~]#cp fs_module.jar <sub>:sub:`~``}

The jar_files folder is located in dax package at the path dax/dax/xnat_modules/jar_files. You can download the files from github repository: https://github.com/VUIIS/dax .

5. Run xnat update

[root@xnat-server ~]#cd ${XNAT_HOME}
[root@xnat-server ~]#bin/update.sh -Ddeploy=true

6. Run sql update

[root@xnat-server ~]# cd ${XNAT_HOME}/deployments/[xnat.project.name]/
[root@xnat-server ~]# psql -f sql/[xnat.project.name]-update.sql -U [db-user] [db-name]

7. Start tomcat

ON XNAT webapp:

1. Log onto XNAT as admin
2. click Administer > Data types
3. click Setup Additional Data Type
4. for fs:fsData

4.a) select fs:fsData and valid without adding anything at first.

4.b) Come back to the new types and edit the fields:

enter "FreeSurfer" in both Singular Name and Plural Name field
enter "FS" in Code field

4.c) Edit the “Available Report Actions” by adding delete if you want to be able to delete assessor with the following values:

Remove Name: delete
Display Name: Delete
Grouping:
Image: delete.gif
Popup:
Secure Access: delete
Feature:
Additional Parameters:
Sequence: 4

4.d) click submit and then accept defaults for subsequent screens

5. for proc:genProcData

5.a) select proc:genProcData and valid without adding anything at first.

5.b) Come back to the new types and edit the fields:

enter "Processing" in both Singular Name and Plural Name field
enter "Proc" in Code field

5.c) Edit the “Available Report Actions” by adding delete if you want to be able to delete assessor with the following values:

Remove Name: delete
Display Name: Delete
Grouping:
Image: delete.gif
Popup:
Secure Access: delete
Feature:
Additional Parameters:
Sequence: 4

5.d) click submit and then accept defaults for subsequent screens

You are now ready to use the two assessors fs:fsData and proc:genProcData