Converter / Roi Volume / AimsVoiStats

Questions about BrainVisa usage and installation

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LaurieV
Posts: 2
Joined: Fri Mar 08, 2013 10:10 am

Converter / Roi Volume / AimsVoiStats

Post by LaurieV »

Dear all,

I am a new user and I would like to convert my pictures.ima into pictures.nii in order to extract the volume of the region of interest that I drew on anatomist.
The problem is that the option in Tools / Converters : Graph To Volume Converter does not work everytime (bug software I do not have the hand anymore and finally, only the creation of a file.nii.minf).
I have downloaded the version 4.3.0 but I have the same problem. Also I have another problem with the update database. Here you can find the message in the bash after the execution of the software Brainvisa :

/usr/local/brainvisa> ./BrainVISA
qt backend 'pyqt'
/usr/local/brainvisa-4.3.0/lib/python2.5/site-packages/matplotlib/lines.py: inconsistent use of tabs and spaces in indentation
/usr/local/brainvisa-4.3.0/lib/python2.5/site-packages/matplotlib/mlab.py: inconsistent use of tabs and spaces in indentation
Loading toolbox brainrat
Loading toolbox connectomist
Loading toolbox cortical_surface
Loading toolbox data management
Loading toolbox datamind
Loading toolbox editors
Loading toolbox freesurfer
Loading toolbox morphologist
Loading toolbox structural_analysis
Loading toolbox tools
Loading toolbox viewers
Loading toolbox My processes
light mode
scheduler type: basic, number of cpu: 12
Local transfer
Local transfer
The log file for this session is '/home/laurie/.brainvisa/brainvisa16.log'
Database /usr/local/brainvisa-4.3.0/share/brainvisa-share-4.3 must be updated
because the database file is too old.
/usr/local/brainvisa-4.3.0/brainvisa/toolboxes/cortical_surface/processes/structural_analysis/group_analysis/projAverageVolumes.py: inconsistent use of tabs and spaces in indentation
/usr/local/brainvisa-4.3.0/brainvisa/toolboxes/morphologist/processes/Sulci/Recognition/recognition_error.py: inconsistent use of tabs and spaces in indentation
/usr/local/fsl/data: parse directories and insert items
/usr/local/fsl/data: 4 files are stored as 4 DiskItems in 0 seconds

In addition, when I managed to obtain the .nii (just some pictures) the command AimsVoiStats -i image.ima -v image.graph -o stats.txt does not work.

I hope I was clear enough. Thank you in advance.
Laurie
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Yann Cointepas
Posts: 316
Joined: Tue Jan 20, 2004 2:56 pm
Location: Neurospin, Saint Aubin, France
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Re: Converter / Roi Volume / AimsVoiStats

Post by Yann Cointepas »

Hi Laurie,

If you only need to use the result of AimsVoiStat, you shoud use AimsRoiFeatures because it is a replacement to AimsVoiStat and you can use either an image or a Graph as ROI (i.e. you do not have to convert). But, in order to investigate the conversion bug anyway, we would need one of your ROI graph that cannot be converted.

The error messages are due to some processes that have a Python specific syntax problem (probably due to the use of several text editors to modify them). It should do no harm unless you need these processes (either directly or via a pipeline).

Best regards,

Yann
LaurieV
Posts: 2
Joined: Fri Mar 08, 2013 10:10 am

Re: Converter / Roi Volume / AimsVoiStats

Post by LaurieV »

Thanks you very much Yann,

I solved the problem in the following days by using the command AimsRoiFeatures.
And about the conversion bug, I realized that my "directory path" was too long, so conversion problem also solved.

Yours sincerely,
Laurie
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