Quan La on 23 Jul 2008 19:21:20 -0700

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[PLUG] One-Day Linux Job Offer at Jefferson Medical College

Dear PLUG members,


The Dr. Tracy Lab at Thomas Jefferson University/Jefferson Medical College (in Center City, Philadelphia) is looking to hire a Linux specialist for a few hours to help compile and run a neuroimaging program called Brainscape 4dfp.  We are trying to compile the program in both Ubuntu 8.04 and Red Hat Linux v4.2 but ran into some problems and need assistance in troubleshooting.  In particular, we are getting errors trying to run the ‘make’ function and ‘makefiles’.


If interested, please read the compilation instructions at the bottom of this e-mail.  If you feel that you can help, contact Quan at (215) 955-8992 between the hours of 9:30am-5pm.  We can send you the source files if you would like to try to compile the program on your own computer first. 


Compensation is negotiable.  The Tracy Lab is located in:


College Building, Rm. 518

1025 Walnut Street (cross-streets are Walnut Street and 10th Street)

Philadelphia, PA 19107


Best wishes,






Make instructions follow.

Three key environmental variables must be set for correct compilation and operation:

NILSRC      directory in which the executables will be compiled

RELEASE     directory where executables will reside

REFDIR      directory that will contain (4dfp format) atlas representative target images. $REFDIR is ~600 MB and has to be downloaded (see below).


It is recommended that the linux .login (startup file) be modified to set the above three environmental variables.  The login procedure should also be modified to include $RELEASE in environmental variables PATH.  The system administrator performing the nil-tools install should be a member of group ‘program’.


1.  Make sure environmental variable $NILSRC is properly set.

Put nil-tools.tar in $NILSRC

cd into $NILSRC and untar nil-tools.tar


2.  Make sure environmental variable $RELEASE is properly set.  Run make_nil-tools.csh.  This will take a couple of minutes.  Check for errors.  You may ignore warnings about time stamps and potentially incomplete makes.  When make_nil-tools.csh is done, all compiled executables should be in $RELEASE.


3.  Put 4dfp_scripts.tar into $RELEASE.  cd into $RELEASE and untar 4dfp_scripts.tar


4.  Download refdir.tar off the web at ftp://imaging.wustl.edu/pub/raichlab/4dfp_tools/

Make sure environmental variable $REFDIR is properly set.

$REFDIR should be at least 1 GB.

Put refdir.tar in $REFDIR and untar.

Run link_711 (script to set up links in $REFDIR that identify atlas representative image masks).


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