.brains2rc (Re: [Brains-users] Error message during measurementof T50 volumes)

[Eugene Zeien]

We are no longer building RH9 rpms.
A "stable" release is on the horizon for RedHat 3, RedHat 4, and SGIs.
To update BRAINS for RedHat9, you'll have to build your own:
http://www.psychiatry.uiowa.edu/wiki/index.php?title=BRAINS_GETTING_STARTED#Building_BRAINS

Christoph Christmann wrote:
> Looking at the file server I can only find a RH version from July 2005. 
> Is the version from January a stable one?
> 
> Best
> 
> Christoph
> 
> Index of /BRAINS/files/StableRelease
> 
>  Name                    Last modified      Size  Description
> 
>  Parent Directory                             -
>  BRAINS2_Users_Guide.pdf 10-Jun-2005 08:04  6.2M
>  BRAINS2_Users_Guide.ps  10-Jun-2005 08:04  196M
>  FedoraCore3/            04-Jun-2005 15:57    -
>  MacOSX_10.3/            10-Jun-2005 16:12    -
>  MacOSX_10.4/            02-Jun-2005 23:06    -
>  RH9/                    27-Jul-2005 11:17    -
>  RHEL3.x_32/             27-Jul-2005 11:17    -
>  RHEL4.x_32/             03-Jun-2005 12:47    -
>  RHEL4.x_64/             27-Jul-2005 11:15    -
>  SGI/                    08-Aug-2005 10:52    -
> 
> Index of /BRAINS/files/StableRelease/RH9
> 
>  Name                                     Last modified      Size  
> Description
> 
>  Parent Directory                                              -
>  brains2-RedHat9-20050603-042442.i386.rpm 03-Jun-2005 04:27   49M
>  brains2-RedHat9-20050727-045902.i386.rpm 27-Jul-2005 11:17   48M
>  brains2_RedHat9_20050603.042442.tar.gz   03-Jun-2005 04:27   50M
>  brains2_RedHat9_20050727.045902.tar.gz   27-Jul-2005 11:17   48M
> 
> At Wednesday 22.02.2006 16:23, Eugene Zeien wrote:
> 
>> Ah.  You are using an older version of BRAINS.
>> The syntax of the .brains2rc file changed in... January 2006?
>>
>> I do not see any evidence that the last 2 variables existed.
>> B2_SCV_FILE, B2_SSM_FILE
>> I think the best you can hope for is to set the directory where
>> those data files are written with B2_GLOBAL_DATA_DIR
>>
>> Christoph Christmann wrote:
>>
>>> Hi all,
>>> regarding the config files I noticed that the general config file (in 
>>> /opt/brains2/bin) has a different syntax. Instead of
>>>
>>>>   B2_EVAL_TCL "B2_GLOBAL_DATA_DIR" "set B2_GLOBAL_DATA_DIR 
>>>> /raid0/data/new_data/brains2 ; "
>>>
>>>
>>> it seems to be necessary to use
>>> B2_GLOBAL_DATA_DIR /home/morpho/brains2_data
>>> Otherwise brains2 reports an error (unknown command...)
>>> However, setting the parameters as follows
>>> # set directory where scripts are saved
>>> B2_WORK_DIR ${HOME}/morpho/scripts
>>> # set global data directory
>>> B2_GLOBAL_DATA_DIR /home/morpho/brains2_data
>>> # redirect brains2 meausres
>>> B2_SCV_FILE ${HOME}/data/Class_Volumes
>>> B2_SSM_FILE ${HOME}/data/Surface_Measures
>>> results in
>>> 1. The first two commands are executed
>>> 2. The last two commands result in error reports
>>> 3. An additional error occures, e.g. the directory where the NET 
>>> information is stored (usually /opt/brains2/bin/net) could not be set.
>>> Therefore we abstained to use this configuration file so far. 
>>> Nevertheless, we would be happy to use a correct version in order to 
>>> prevent the known error messages during the segmentation process.
>>> Thanks in advance for any hint
>>> Christoph
> 
>