There are two standard ways that data can be uploaded to CHPC. Firstly using the command line, and secondly using a GUI (Graphical Users Interface.) The GUI method will be explained here.

Very Important Note:
It is very important that you never give you password to anyone. Rather let them apply for their own login, as this could compromise the security not only of your login, but the entire CUBIC group! Remember, the more usernames we have in the CUBIC group, the more funding we can apply for! This is beneficial for everyone.

SCP using a GUI in Windows
There are various tools available that can relieve the hassle of copying files over SSH. WinSCP and Bitvise Tunnler are two options for Windows. Here is a tutorial explaining how to use WinSCP in detail. For host, use Set the port to 22 .

SCP using a GUI in Linux
Under Linux, secpanel can be used.

Here is a screenshot of how I setup my connection:


Here are some links I have found helpful in getting on the move with UNIX/Linux. Always remember if you want to do something, try googling it first. You will be able to learn just about anything Unix related if you just ask google.

Here are some links to get you started (I will be adding to this list in the coming months:

Beginner’s UNIX tutorial
Easy Shell Scripting
UNIX History on Wikipedia
Introduction to BASH programming

Running FSL on the cluster

Posted: June 7, 2010 in HOW-TO's
Tags: , , ,

First login on cluster using:

ssh -X


cd /SCRATCH4/cubic/vault/

ls” should show you the RESEARCH directories. They are named in chronological order. This is just as the radiographers load the data on the CUBIC data disc. Please note that you won’t be able to edit the files, just copy them. This is intended to prevent mishaps!

Locate your files and “cp” them over to your space on the /SCRATCH4/cubic/. Please create a directory if there is not already one for your own use, such as:

mkdir /SCRATCH4/cubic/yourusername

The “cp” command should look like: “cp -vr vault/RESEARCH1/CONFLUENCE/* yourusername/” if you are in the /SCRATCH4/cubic directory. Please note this copy can take some time. If you terminate your ssh session, the “cp” command will stop.

There are a few ways of getting around this:

You can run “screen” for example. Press space bar, then run the above command. Then you can press “Ctrl-A d” and it will run in the

At the moment the only converter working on the cluster is “mri_convert” on the command line.

It works like this:
mri_convert [options]

Run “”mri_convert“” for further details. This can be a bit painful
process. Sadly we could not compile the other converters to date due to too many dependencies… watch this space…


ssh chpcsp01 or chpcsp02 to get to a node that is not used so
that you can “preprocess” heavy duty things that you dont want to
“clsterize” just yet. Works well fgor debugging. One cannot msub from
these nodes, nor run fsl! So be aware!

Now “cp” the “fsl_sub” script in
/export/home/splessis/dropbox/scripts/fsl_sub by typing :

cp /export/home/splessis/dropbox/scripts/fsl_sub $FSL_DIR/bin

Now “ssh” to the login02 node by typing “exit” if you are still on one of the preprocessing nodes. (chpcsp01 an chpcsp02)
run fsl& from the directory in which your files are.

Proceed as normal. The script is made to automatically detect the
environment and run the cluster accordingly.


(An mri_convert shell script would be appreciated…)

FSL course

Posted: November 22, 2009 in Courses

Thank you once again for everyone’s valuable support on our first ever FSL course. It was inspiring to see such enthusiasm and willingness to learn! We hope to continue to support our forming imaging community here in Cape Town, and in doing so help establish a well grounded working environment for our research. We hope to achieve this by regular online support, an mailing-list and further such imaging courses.

There have been many requests for further written tutorials in the command line, fMRI and DTI analysis. To start us off, here are a few useful links to sites related to our course and some interesting information! Please feel free to suggest further topics for us to cover!

Beginner’s UNIX tutorial
Information Science: Primer on Wikipedia
fMRIb hompage
CHPC’s Platform specifications
FSL’s Mailing List
The Salmon Activation

More is to follow!