Index
1. Medical Image Format FAQ
[http://www.dclunie.com/medical-image-faq/html Medical Image Format FAQ]
2. CVS Checkout
You can checkout the FreeSurfer source code from the NMR center using local CVS access or remotely by using SSH as the CVS remote connection method.
2.1. Local CVS Access
The CVS repository is /space/repo/1/dev. Use this as your CVSROOT. You can either set it as an environment variable:
setenv CVSROOT /space/repo/1/dev
or specify it in the checkout command with the -d option. Note that the CVS root is cached in a CVS checkout directory, so if you choose to use the -d method, you will only have to do it once during your first checkout.
Check out the code with the CVS checkout command. The archive name is dev.
cvs checkout dev
or
cvs -d /space/repo/1/dev checkout dev
This will copy the entire archive to your directory, creating a directory called dev/. Now set up your environment to use this dev directory by running the script in dev/:
{{{cd dev source set_dev_env_to_here.csh}}}
2.2. Remote CVS Access
Tell CVS to use SSH to access the archive by setting the following environment variable:
setenv CVS_RSH ssh
Use the following string as your CVS root:
:ext:USER@MACHINE.nmr.mgh.harvard.edu:/space/repo/1/dev
Where USER is your username and MACHINE is one of the NMR machines visible to the outside, i.e. gate, entry, or door. Then use the CVS commands normally.
Note that using this method makes an SSH connection for every CVS command, and you will be required to enter your password every time. You may want to look into a utility to automatically authenticate SSH connections, such as SSH agent.
3. Building