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

[Eugene Zeien]

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
> 
>> This line (if it weren't commented out) would configure where brains2
>> scripts are stored.
>>
>> # Default Location to place batch files
>> # B2_EVAL_TCL "B2_WORK_DIR" "set B2_WORK_DIR ${HOME}/<username> ; "
>>
>> If you wish to change these for everyone using your computer,
>> edit /opt/brains2/bin/brains2rc.  If you want to change these settings
>> for yourself only,
>>   copy these lines into your ~/.brains2rc
>>   delete the # for the "B2_WORK_DIR" line
>>   and change to locations of your choice
>>
>> For example,
>>
>>   B2_EVAL_TCL "B2_GLOBAL_DATA_DIR" "set B2_GLOBAL_DATA_DIR 
>> /home/simone/brains2_data ; "
>>   B2_EVAL_TCL "B2_WORK_DIR" "set B2_WORK_DIR /home/simone/scripts ; "
>> (might want to 'mkdir /volume/storage/location /home/simone/scripts' 
>> first) ;-)
>>
>> Simone Brockman wrote:
>>
>>> It seems I spoke too soon about not having any further problems...
>>> When I go to run the t50 volumes, I get an error message both when I 
>>> save it to run later and if I try to run it straight away. The error 
>>> message when I try to save occurs after I try to save the 
>>> _t50vol.brains2 in the default location of the home directory and reads
>>> "Failed to save the check measurement script! Verify there that there 
>>> is a ...ACPC/root directory."
>>> and the error message when I try to run interactively occurs when I 
>>> try to select the update button on the Check T50 Volumes dialogue box 
>>> and reads
>>> "Failed to open global raw volume data file  
>>> /raid0/data/new_data/brains2/t50/t50_volumes_raw.dat.
>>> I have the option to modify the Global Data File before running the 
>>> T50 Volumes but it seems to be looking for something my system 
>>> doesn't have. Isn't /raid0 an IPL specific directory structure? Am I 
>>> missing a file or have I done soemthing incorrectly in preceding steps??
>>> Many thanks for your advice
>>> Simone
>>> UWA Perth
>>> Western Australia
>>>
>>> _______________________________________________
>>> Brains-users mailing list
>>> Brains-users at www.psychiatry.uiowa.edu
>>> http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users
>>
>>
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> 
>