BrainVISA

Thanks for the updates. We need to plan our next BrainVISA-based developments (if any). Does this mean that in the future, we'll download a virtual machine in which we'll be able to install our development environment and execute IntrAnat? Do you have an approximate timeline for this future VM relea...

Dear colleagues, Is there still some resource available for the support of BrainVISA? Are there clear plans to keep on updating this software in the future? Or should we start porting the BrainVISA-based tools to a different platform? The last release from 2018 (4.6.1) still lacks some critical patc...

Hello, We have one patient for which we get this error: Process Hip-Hop Cortical Parameterization started on 2019/06/04 15:11 progress: 0.0 / 100 ... progress: 0.0 / 100 ... Changing Referential... Projection Done Dilation Erosion Done Topological correction... 1797 vertices have the texture value 1...

Hello, We're still getting the same error message with some patients: Process Import FreeSurfer grey/white segmentation to Morphologist started on 2019/06/04 14:49 Convert .mgz to .nii with FreeSurfer Import data into database with brainvisa ontology filein : /tmp/bv_17664_8.nii fileout : /mnt/epile...

Removing all these libraries fixed python.
Thanks!

Detail of the packages that were upgrade yesterday, causing BrainVISA to crash: 2019-02-26 08:30:03 upgrade dkms:all 2.2.0.3-2ubuntu11.5 2.2.0.3-2ubuntu11.6 2019-02-26 08:30:04 upgrade shim-signed:amd64 1.33.1~16.04.3+15+1533136590.3beb971-0ubuntu1 1.33.1~16.04.4+15+1533136590.3beb971-0ubuntu1 2019-...

Hello After a recent upgrade of Ubuntu 16 packages, BrainVISA 4.6.1 and the most recent 4.6.1 stopped working. It already happens on two of our computers: a native Ubuntu 16, and my Ubuntu 16 running on Windows 10/WSL. After setting up the brainvisa python environment (source /path/bv4.6.2/bin/bv_en...

Hello, When the BrainVISA database is located on a Windows share mounted as CIFS on Linux, shelltools.cp crashes. The reason is that Linux cannot set properly the file access rights on a CIFS mount, and shutil.copy/shutil.copy2 crash instead of nicely handling the problem. In such configuration, I c...

Hi Denis, It doesn't crash, but in fact it doesn't work very well either. After taking an abnormally long time to run, the MarsAtlas segmentation that comes out of it is totally wrong on the left hemisphere (but correct on the right). The left hemisphere also looks abnormally inflated compared to th...

Indeed, it seems to be working a lot better.
Thanks for the quick fix!

It was generated with FreeSurfer 6 indeed. But I think we have been importing other FreeSurfer 6-processed patients previously without any problem.

Erratum: It does NOT work from Brainvisa, I get the same error message: Cannot insert "/home/ftadel/IntrAnat/brainvisa_db/subjects/0001BAR_27112016/t1mri/FreesurferAtlaspre_2016-11-27/default_analysis/nobias_0001BAR_27112016.nii" because its uuid is in conflict with the uuid of another fil...

It seems to work if I run it from BrainVISA, with the process FreeSurfer > Import > Import FreeSurfer grey/white segmentation to Morphologist. I select two entries only: - T1_orig: /home/ftadel/IntrAnat/freesurfer/subjects/0001BAR_27112016/mri/orig.mgz - T1_output: /home/ftadel/IntrAnat/brainvisa_db...

PS: if I update the database, I get messages like this: /home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/soma/html.py:104: UnicodeWarning: Unicode equal comparison failed to convert both arguments to Unicode - interpreting them as being unequal u'ô', u'î', u'û', u'ù', u'ö', )]) ...

It looks like I am getting this error with most of the subjects now... this is totally blocking us for adding new patients to our SEEG database... This was working before. I'm not sure if it changed after a change I made, or after I upgraded to the last compiled version you sent me. Here is another ...

It does look normal, and it used to work on this patient, with the same FreeSurfer segmentation folder.
I sent you the FreeSurfer output by email.