BrainVISA

Hi, The BV process that you mentioned "Volume series to single file" seems to work. To select a serie of images, you just have to select one file and brainvisa takes into account all the serie. Indeed, it is not very clear that the selection works as only the file you selected is visible i...

Hi Renaud,

You can use the findDiskItems of brainvisa databases :
neuroHierarchy.databases.findDiskItems({"_type" : "T1 MRI Bias Corrected"})

Dominique

oups! Yes that's what I wanted to say

Hi Isabelle, Can you type in the name of the protocol and the subject in the corresponding field ? And does it work when you do that ? Actually, Brainvisa suggests name for protocols and subjects if you already have same type data in your database. If this is the first data of that type that you imp...

Hello,

It seems that left_white_sulci and right_white_sulci are not optional even if they are indicated as optional in the process "create Label texture". Were these parameters filled when you ran the process ?

Dominique

Hi,

Are you sure of the identifier of the process that you give to runProcess function ? It should be either the process filename without extension or its english name.
Is this process available when you run brainvisa in graphical mode ?

Dominique

Hello, it seems that you have not the same version of BrainVISA on the two computers or at least you have an old database in computer A. Indeed the data path on computer A correspond to the old organisation of BrainVISA database (protocol/subject/anatomy/image). It was used in BrainVISA 3.0. Whereas...

A minor 3.1.6 update has been released in the download section. It is a bugfix update.
It includes more recent version of Numpy (1.3.0) and Scipy (0.7.0). The Windows package now uses Python 2.5 like the Linux and MacOs packages.

Hello,

I cannot reproduce this problem on our Mac but it is not the same OS.
What is the format/extension of the file you try to import ? Maybe it is a file without extension (format dicom for example) and so brainvisa cannot recognize the format.
Did you try with another file ?

Dominique

Hi Tony, It seems that your data files are not in a BrainVISA database (mri = C:\BrainVisa\cartopac_02_19\01.nii, mri_corrected = C:\BrainVisa\cartopac_02_19\01_corr.nii). I guess you have not used the green database button to select these parameters but the filesystem button, don't you ? It is not ...

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 ou...

Hi, 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 s...

Hi, To know what are the parameters, you can run Brainvisa in normal mode (with the graphical interface) and open the process "T1 MRI/Segmentation Pipeline/T1 Pipeline 2007". The name of the parameters in the graphical interface are the same as the parameters that you can pass to the metho...

Oh, I see. The step "split brain mask" automatically generates the split brain mask, so you mustn't run it *after* having corrected manually the mask, else you indeed erase your corrected mask. If you are using the process "T1 pipeline 2007", after having corrected manually your ...

Yes, in the process "T1 pipeline 2007", the split brain mask "split_mask" is generated in the step "Split Brain Mask" and it is used as an input named "brain_voronoi" in the step "Ana Get Opened Hemi Surface", which generates the hemisphere meshes. Y...