vbbatch

vbbatch is a command line tool that allows you to submit a bunch of command lines to the queue. You just need to specify the command line and a list of files to be substituted into the command line (wherever the string FILE appears). For safety, by default vbbatch just shows you the commands. If you're happy with what you see, use the -r flag to make it happen.

Here's the help text:

VoxBo vbbatch (v1.8.5/Jun 14 2011)
usage:
  vbbatch -c <command> [<file> ...]
flags:
  -c "command"   command line to execute (should be in quotes)
  -p <pri>       set job priority
  -xfile <str>   use str instead of FILE
  -xind <str>    use str instead of IND
  -xbase <str>   use str instead of BASE
  -m <maxjobs>   maximum number of concurrent jobs at full priority
  -r             really run it, don't just show the commands
  -req <req>     add a requirement (you'll know if you need it)
  -i             interactive mode (ask for each file)
  -d <n>         add a bunch of dummy files (see below)
  -sn <seqname>  sequence name visible in queue
  -jn <jobname>  job names visible in queue (can use FILE, IND)
  -f <seq>       flush private sequence
  -a <seq>       append to private sequence
  -s <seq>       submit private sequence
  -l <dir>       directory for storing log files (will be created
                 if necessary)
  -e <email>     address for notification, use -- for no email
  --run=<n>      don't queue, run now on n cores
  -h             show help
  -v             show version
notes:

  In your command, the token FILE will be replaced with each file you
  specify.  The token BASE will be replaced with each filename, but
  with the extension stripped off.  The token IND will be replaced
  with an index, starting from 000.  If you actually need the tokens
  FILE, IND, or BASE in your command, you can change what vbbatch
  replaces using the -xfile, -xind, and -xbase flags.
  
  maxjobs defaults to 10
  
  The -f, -a, and -s options allow you to build a compound
  batch job in pieces, and then to submit the whole thing as
  one sequence.  Use -f to first flush it (just in case), then
  call vbbatch as you normally would, but use -a to append the
  jobs to your private sequence, and finally use -s to submit
  the whole thing.
  
  The -r flag is there to encourage you to check the generated command
  lines before you really submit.  Run vbbatch without it, and you'll
  see all the commands that will be run.  If you like what you see,
  run it again with -r.
  
  The -p flag can take a numeric priority from 0 to 5 or a scheduling
  policy (run vbtool pri for more info).

  If --run is specified without =n, the default is the total number of
  available cores minus 1 (or 1, if that would be 0).  Note that even
  if you use --run, you still have to include the -r flag to indicate
  you really want to run the jobs, not just see them.

  The -d flag lets you create "dummy" files, with the filenames just
  being the numbers from 0 to n-1.  Usually you would use it with IND,
  not FILE.

examples:
  Run myscript.sh on all your subjects' Anatomy directories:

    vbbatch -c "myscript.sh FILE" study*/sub*/Anatomy -r

  Run myperms.sh 1000 times at low priority, with different output
  files:

    vbbatch -c "myperms.sh results_IND.nii.gz" -d 1000 -r -p xnice