BrainVISA

Hi, In Morphologist, the segmentation part is not lateralized, and thus will process a reversed image the way you expect. If I understand this is what you see, the segmented image and extracted folds show the reversed asymmetry you were expecting. Now the sulci recognition is using an asymmetric atl...

Yes the next distribution will be VM-based, using either Singularity or VirtalBox (both will be supported, maybe docker later). It will be possible to build another image with added libraries and toolboxes, but the modular distribution as it was using the installer will be lost, because VM images do...

Hi, Brainvisa is not dead but we struggle to perform maintenance and releases. We are not many people working on it and we have difficulties to handle system compatibilities for every system / distribution. That's why we will release the next version of brainvisa as a container or (and) virtual mach...

Hi, The energy_plot_file.nrj is a record of the global (whole hemisphere) energy across the optimization, it does not contain the local energies. I don't remember any process providing this locally. It could be done of course because they are used during the identification process, but it's not read...

Hi, Well 4.5 is rather old and we cannot guarantee a maintenance on it. You can open the log window and look for the error in the process execution, it may contain more details on the command execution and its failure, but as I said, we will not fix it on 4.5. Especially if it works in 4.6 this prob...

We have finally found why the Mac version doesn(t run on recent Macs. A part of the python package was missing. I have put a new tarball of the python package here: ftp://ftp.cea.fr/pub/dsv/anatomist/updates/4.6.1/osx/python.tar.gz It should be un-tared in the root directory of the BrainVisa install...

Hi, This old process was designed for the oldest models (ANN), and thus is using the ANN model file (not used in SPAM method) to provide a recognition energy which will not be useful to you. Anyway I think the problem is in the kind of labels the process is using: labels are stored in attributes in ...

Hi, Oh you are right, the libCifti didn't get into 4.6.1 distribs. We will fix that for the next one. In the meantime I have put the libs in ftp://ftp.cea.fr/pub/dsv/anatomist/updates/4.6.1/<system>/lib/ (replace <system> with win64, osx, linux64-glibc-2.23 etc). For linux there are 3 times the same...

Hi, We have been reported problems on recent Mac systems that we don't have on hand. I could observe it once but could not solve it on the fly. It seems that on some of these systems, a different python installation (the system one) gets loaded when we call the one from brainvisa, regardless of PATH...

Hi François,
A program run by the process has crashed, the log should provide more details (the exact command which was run with its parameters).

The cingular pole extraction seems to cause problems on this specific patient. Do the segmentation and meshes look OK ?
Denis

In this case, the window should probably be set in the referential you consider to be Talairach (usually it's the default red one). You can assign a referential to a window just as to an object: window.assignReferential(target) It doesn't need to be the referential of an object, but there has to be ...

OK.
Oh there is also a libpthread.so which should be removed (we'll have to check all libs next time).
Denis

Hi, I could reproduce (more or less) the problem in a docker container (it seems a bit random, sometimes works, sometimes crashes). I guess you are using the ubuntu 16 variant of brainvisa binary distribution (glibc-2.23), right ? It appears that some libs got included in this package by accident th...

Hi Olivier, If you are running this exact code, then it's normal since all objects have been assigned the same referential (source), so whatever the transformations to other referentials (target), it doesn't change anything for them. If one object (let's say aSTS) is assigned the target referential,...

Hi, I haven(t checke precisely right now, but I guess the shift is due to transformations in the original image header not being copied to the sulci image. To fix this you can write a little python script using the pyaims libraries in brainvisa: from soma import aims t1_image = "path_to_t1.nii&...