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

[Christoph Christmann]

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
>
>_______________________________________________
>Brains-users mailing list
>Brains-users at www.psychiatry.uiowa.edu
>http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users

-- 
Christoph Christmann                  christma at as200.zi-mannheim.de
Psychologist, MEE                     Fon/Fax +49 621 1703 63 18/05
Central Institute of Mental Health    http://www.zi-mannheim.de
Department of Clinical                  D-68159 Mannheim J5
and Cognitive Psychology                       

**********************************************************************************************
IMPORTANT: The contents of this email and any attachments are confidential. They are intended for the 
named recipient(s) only.
If you have received this email in error, please notify the system manager or the sender immediately and do 
not disclose the contents to anyone or make copies thereof.
*** eSafe scanned this email for viruses, vandals, and malicious content. ***
**********************************************************************************************