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…)


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