Duke-UNC Brain Imaging and Analysis Center
BIAC Forums | Profile | Register | Active Topics | Members | Search | FAQ
Username:
 Password:
Save Password   Forgot your Password?
 All Forums
 Support Forums
 Analysis Software Support
 Processing on the p670 (update)		  New Topic  Reply to Topic
 Printer Friendly
Author Previous Topic Topic Next Topic  

jimmy.dias
BIAC Alum

USA
210 Posts
Posted - Nov 18 2003 :  10:36:21 PM  Show Profile  Visit jimmy.dias's Homepage  Reply with Quote
p670 users,

Scripts on the p670 are now available for the following processing steps:

tralign
motioncorrect
coregister
coreg_normalize
normalize
smooth

Each of these scripts are basically command line interfaces to SPM99 routines. Each script requires at a minimum a valid BXH header + the functional data you are processing on as its input. Please view the help for information on what each script does and how to use each script by doing the following:
<program name> --help
e.g.
[dias@golgi: ~/net/huxley/data] $ tralign --help

All these scripts and the programs each require should already exist in your path.

For those of you who have been using the scripts within the last month or so, I've changed the command line interface slightly so that specification of the anatomical directory is done using --anatglob or -a. Please make sure you update your batch scripts accordingly.

Enjoy!
Jimmy
Edited by - jimmy.dias on Nov 19 2003 08:37:17 AM

jimmy.dias
BIAC Alum

USA
210 Posts
Posted - Nov 24 2003 :  10:35:59 PM  Show Profile  Visit jimmy.dias's Homepage  Reply with Quote
p670 users,

Each of the processing scripts above have a default set of parameters that can be viewed at /etc/SPM99_procd.conf on Golgi. Before running any of the above scripts, please take a couple of minutes to take a look at the above file and see what options I've selected.

For advanced users, you can now specify your own parameter file by using the --config=s option. I would suggest copying the global configuration file to your home directory, and modifying it appropriately. Each of the above scripts have some built-in error checking to them so as to prevent you from specifying values that are too far-fetched. If you need theses ranges to be increased, let me know...

Note: For the --config option, you have to specify the full path name to the modified config file. Substituting ~/ for /home/dias/ will not work for this option.

For example,
tralign -r 'Func/20030402_45620/run004_0*' -D 5 --save --config=/home/dias/myconfig.conf
will work and

tralign -r 'Func/20030402_45620/run004_0*' -D 5 --save --config=~/myconfig.conf
will NOT work.

Enjoy,
Jimmy
Edited by - jimmy.dias on Nov 24 2003 11:18:41 PM
Go to Top of Page
  Previous Topic Topic Next Topic  
 New Topic  Reply to Topic
 Printer Friendly
Jump To:
BIAC Forums © 2000-2010 Brain Imaging and Analysis Center Go To Top Of Page
This page was generated in 0.42 seconds. Snitz Forums 2000