if isinstance( processIdClassOrInstance, basestring ) and minfFormat(
processIdClassOrInstance )[ 1 ] == minfHistory:
api.py (98) in minfFormat:
source = BufferAndFile( open( source ) )
ERROR unexpected EOF while parsing (<string>, line 1)
--------------------------------------------------------------------------------
SyntaxError
neuro.py (173) in main:
exec f in globals(), localsStartup
Exception exceptions.AttributeError: "'NoneType' object has no attribute 'currentThread'" in <bound method ThreadSafeSQLiteConnection.__del__ of <soma.databases.sqlite_tools.ThreadSafeSQLiteConnection object at 0xa954b0c>> ignored
Exception exceptions.AttributeError: "'NoneType' object has no attribute 'currentThread'" in <bound method ThreadSafeSQLiteConnection.__del__ of <soma.databases.sqlite_tools.ThreadSafeSQLiteConnection object at 0xaa2d90c>> ignored
Exception exceptions.AttributeError: "'NoneType' object has no attribute 'currentThread'" in <bound method ThreadSafeSQLiteConnection.__del__ of <soma.databases.sqlite_tools.ThreadSafeSQLiteConnection object at 0xa6cbacc>> ignored
The error message doesn't seem to be in relation with the command you passed to brainvisa at startup. I think the error is about a process bv_pipeline.py that you put in your $HOME/.brainvisa/processes directory.
By the way, you also have a syntax error in the your command line, you have mixed simple quotes and double quotes (' and "). You should write this :
brainvisa -b -c 'defaultContext().runProcess("ImportT1MRI", input="/home/jinju/t1_icbm.mnc", output = { "protocol": "a test", "subject": "a ddd", "acquisition": "default_acquisition"} )'
And last advice, maybe you should avoid using space in the protocol and subject names. This will create directory names with space which is not very practical...
raise Exception( HTMLMessage(_t_('argument <em>%s</em> is mandatory') % name) )
Exception exceptions.AttributeError: "'NoneType' object has no attribute 'currentThread'" in <bound method ThreadSafeSQLiteConnection.__del__ of <soma.databases.sqlite_tools.ThreadSafeSQLiteConnection object at 0x9d1fb0c>> ignored
Exception exceptions.AttributeError: "'NoneType' object has no attribute 'currentThread'" in <bound method ThreadSafeSQLiteConnection.__del__ of <soma.databases.sqlite_tools.ThreadSafeSQLiteConnection object at 0x9df890c>> ignored
Exception exceptions.AttributeError: "'NoneType' object has no attribute 'currentThread'" in <bound method ThreadSafeSQLiteConnection.__del__ of <soma.databases.sqlite_tools.ThreadSafeSQLiteConnection object at 0x9a96acc>> ignored
This error message means that brainvisa cannot generate the file name of the output.
Maybe you haven't configured your brainvisa database ? To do that, go to brainvisa => preferences => databases menu and click on the add button. Then you choose a directory for your database, brainvisa will write output data in this directory.
Maybe you haven't configured your brainvisa database ? To do that, go to brainvisa => preferences => databases menu and click on the add button. Then you choose a directory for your database, brainvisa will write output data in this directory.
Don't forget to import the T1 image into your database before running the T1 pipeline: the filename you gave as input "/home/jinju/t1_icbm.mnc" doesn't match the database organization here, so output filenames cannot be generated.
But, as Dominique has pointed out, all this is explained in the docs...
Denis
I also would like to run the processes in batch mode. In particular: Import T1 MRI, Morphologist 2013 and Sulci Recognition.
I have installed BrainVISA 4.4.0.
Is there a tutorial explaining how to set up these scripts? Or, is there an existing script that I could use as a starting point?
I don't remember tutorials cover this topic, now that you say it...
However it is not so difficult to run brainvisa in batch mode: you can do it
in commandline mode,
either using the "brainvisa -b -c ..." mode explained earlier in this post
[*/]
or using the newer command "axon-runprocess" (use it with --help to hget help). It's basically the matter of naming a process and providing parameters. If you need parameters completion and databasing, don't forget to use the --enabledb option. If not, you will have to specify every one of the parameters (there may be many...)
before initializeProcesses(), it will start faster.
Note that importation processes can generally not completely perform input/output parameters completion, because there is no information in the input file name that allows to find out where the imported data should be written.
I can run a .bvproc script in this way: 'brainvisa -r file.bvproc'
I still have a couple of questions:
- Is it possible to update the database using a .bvproc script, or other brainvisa command line options?
- Once a subject is analyzed with the T1 pipeline the files are 'locked'. How can I unlock them without using the graphical interface?