[VoxBo] jobtypes

[Clayton Curtis]

Hi Dan,

I've recently upgraded to 1.8.2 from 1.6.  I'm having problems with  
my dozen or so jobtypes that my lab has developed.  They worked in  
1.6 but for some reason are not working in 1.8.2.  Has anything  
changed about the structure or syntax of voxbo jobtypes?  Or is there  
something special about the way your migrate the jobtypes?  I just  
simply copied them into the jobtypes directory of the new  
distribution.  However, when I  "voxq --jobtypes" I do indeed see my  
jobtypes.

I'm pasting a simple jobtype as an example below, as well as the  
call.  This uses FSL's avwswapdim to reorient 4D files.  The job gets  
submitted to the voxbo scheduler fine but then goes bad.  The error  
message in the voxbo log for that job is simply the output of  
avwswapdim if you don't give it any args or the args are wrong.  And,  
when I run the command outside of voxbo, just using avwswapdim at the  
command line, it works fine.   Other voxbo jobs that came with the  
distribution works fine.

Also, can you point me to documentation on creating jobtypes?

One other suggestion that would be helpful is the addition of a field  
on the webpage for searching for keywords in the mail archives.   
Yeah, I know you can do this in google, but you also get a bunch of  
irrelevant stuff.

Thanks!

EXAMPLE JOBTYPE:
------------------------------
shortname fsl_reorient_4D_img
fullname fsl_reorient_4D_img
description Reorient images into a requested orientation.
invocation commandline
# 0 = input filename
# 1 = output filename
# 2 = first new axis
# 3 = second new axis
# 4 = third new axis
# example of values 2-4: -x -y z would rotate image 180deg around Z-axis
command /usr/local/fsl/bin/avwswapdim $0 $2 $3 $4 $1
requires cpu
#requires fastdisk

------------------------------

EXAMPLE CALL OF ABOVE JOBTYPE
  ------------------------------
PRIORITY 2ls

SEQUENCENAME functional_preprocessing
GLOBALS TRinMS=2000 TRinS=2 HPFilt=-1 LPFilt=-1
FILE DirName=/deathstar/data/Cash/35Cash/rawdata/35Cash/05 
+cbi_ep2d_bold_36sl InFile=Test1 OrigFile=35Cash+05 
+cbi_ep2d_bold_36sl Order=0
fsl_reorient_4D_img $DirName/$OrigFile $DirName/$InFile x -y z

/cc

Clayton E. Curtis, Ph.D.
Psychology & Neural Science
New York University
6 Washington Place, Room 859
New York, NY 10003
Office - 212.998.3730
Lab - 212.998.8347
Fax - 212.995.4562
http://www.psych.nyu.edu/curtislab


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