DSI Studio

This software is installed on the cluster. The DSI Studio project website is: http://dsi-studio.labsolver.org/Home

The software is: Developed by Fang-Cheng (Frank) Yeh, Department of Psychology, Carnegie Mellon University

Supported by Advanced Biomedical MRI Lab, National Taiwan University Hospital, Cognitive Axon Lab, Carngie Mellon University

How to run the DSI Studio Software Interactively

1) Connect to the head node:

$ ssh -Y -C -l <username> psych-o.hpc1.cs.cmu.edu

2) Connect to a node for an interactive session:

[<username>@psych-o ~]$ qsub -I -X

3) Make qt-4.8.5 your default version:

[<username>@psych-o ~]$ module load dsi-studio

4) Run the latest version of DSI Studio:

[<username>@psych-o ~]$ dsi_studio

How to run the DSI Studio Software without Invoking Graphic User Interface (GUI)

1) Connect to the head node:

$ ssh -Y -C -l <username> psych-o.hpc1.cs.cmu.edu

2) Create a pbs script using an installed editor like emacs (see example below):

[<username>@psych-o ~]$ emacs my.example.pbs

3) Submit the pbs script to the job scheduler:

[<username>@psych-o ~]$ qsub my.example.pbs

4) Monitor job queue:

[<username>@psych-o ~]$ qstat

Example PBS Job Script:

##------------------------------------------ Start of DSI Example PBS Script --------------------------------------------------
#PBS -S /bin/sh
 
## Merge stderr to stdout (optional, otherwise they're in separate files)
##Specify the output filename explicitly (optional; the default is named
## from the job ID, in the directory where qsub was run.)
#PBS -j oe /path/to/output/directory/testjob.out
####### OR######.....INSTEAD of above line use following two lines to designate separate out and error files
#PBS -o /path/to/log/directory/nameoffile.out
#PBS -e /path/to/log/directory/nameoffile.err
##Requests 1 node to run 2 process and 2GB of RAM in the queue. #PBS -l nodes=1:ppn=2,pmem=2GB ## Request mail when job ends, or is aborted (optional, default is "a" only) #PBS -m a # To start in a certain directory; you probably need to change. cd /path/to/directory/you/want/to/change/to ## Below are the actual commands to be executed (i.e. to do the work).
## need to load the correct qt module and put the dsi_studio application in your path module load dsi-studio
##Run DSI Studio software without user interface
dsi_studio --action=trk --source=./DWITemplates/templates/CMU-60_2mm_xxxxxxxxbuild.fib.mean.fib.gz

##------------------------------------------ End of DSI Example PBS Script --------------------------------------------------

-- David Pane - 2015-05-05

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Topic revision: r3 - 2017-03-15 - DavidPane
 
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