CONN Toolbox

The Functional Connectivity (CONN)) toolbox for MATLAB is available as an Lmod module on Klone compute nodes.

Use with Lmod

Like all Lmod modules, the conn module is available only on Klone compute nodes, and these commands will not work on the login node.

Checking available versions

Because the module for CONN is installed in the escience hierarchy, its name is prefixed with escience/.

You can check the installed versions as follows:

module spider escience/conn

The output should look a bit like this:

---------------------------------------
  escience/conn: escience/conn/v.22.a
---------------------------------------

    This module can be loaded directly: module load escience/conn/v.22.a

    Help:
      conn-v.22.a

Running CONN

Load the default version with module load escience/conn or load a specific version with module load escience/conn/version.

After loading the module, start matlab and run conn in the MATLAB command window.

Installing different versions via Lmod

You can install different versions of CONN by following the instructions below.

1. Go to https://www.nitrc.org/frs/?group_id=279, choose the version of CONN you want to install, copy the download link to the file, and download the file by running the following command on a Klone login or compute node. We’ll use version 21a as an example:

   mkdir -p "/gscratch/scrubbed/$USER/downloads" && cd "$_"
   curl -LO https://www.nitrc.org/frs/download.php/12426/conn21a.zip
   

   1

   Create the target directory if it does not exist and navigate to it ($_ is a special variable that expands to the last argument of the previous command).

   2

   curl is a program you can use to download files from the web. Replace the URL with the URL for the version of CONN you want to install. The -L option tells curl to follow redirects, and the -O option tells it to save the file to the current directory.

   Tip

   The directory /gscratch/scrubbed/$USER/downloads will expand to /gscratch/scrubbed/(your username)/downloads. This directory is a good place to save files temporarily – see our guide to storage on Klone for more information.

2. Extract the archive and copy the contents to /sw/contrib/mylabname-src/conn/21a (replacing mylabname with the name of your lab):

   unzip conn21a.zip -d conn21a.zip
   # Make sure you include the parentheses around the commands below. Replace "mylabname" with your lab name!
   (umask 002 && mkdir -p /sw/contrib/mylabname-src/conn/21a && rsync -rlHP --chmod=a+rwX conn21a/conn/ $_)
   rm -rfv conn21a.zip conn21a
   

   1

   Extract the CONN archive to a new directory called conn21a.

   2

   In bash, parentheses create a [subshell]((https://tldp.org/LDP/abs/html/subshells.html), which runs the enclosed commands in a new shell session. We want to use it here so that we can temporarily modify the default permissions for new files and directories with the umask command. Your current settings will remain intact when the commands in the subshell are completed.

   3

   We’re running a series of commands here in a [subshell]((https://tldp.org/LDP/abs/html/subshells.html). Let’s break it down:

   4

   Remove the downloaded file and the extracted directory.

3. Use a text editor to create an Lmod .lua module file for the new release with a text editor, using 21a.lua as the filename:

   /sw/contrib/modulefiles/mylabname/conn21a.lua

   help(myModuleName())
   local base = pathJoin(
       "/sw/contrib",
       string.gsub(myModuleName(), "/.*$", "-src"),
       string.gsub(myModuleName(), "^.*/", ""),
       myModuleVersion()
   )
   whatis("Name: " .. string.gsub(myModuleName(), "^.*/", ""))
   whatis("Version: " .. myModuleVersion())
   depends_on("matlab")
   depends_on("escience/spm") -- edit this line to match the name of your SPM module
   append_path("MATLABPATH", base)

   Tip

   If you don’t know how to use a text editor on Klone, you can try nano, which is installed on the system. To create a new file, run nano filename, paste the contents of the template into the file, and save it by pressing Ctrl+O and then Enter. To exit, press Ctrl+X.

4. Check that the module is available and load it:

   module -I spider mylabname/conn
   module load mylabname/conn/21a
   

   1

   Lmod takes some time to cache available modules. You can use the -I option to force Lmod to check for new modules.