Search found 61 matches

by francois
Wed Jun 05, 2019 1:35 pm
Forum: BrainVISA
Topic: ERROR in Cingular Pole Projection 2 System call crashed
Replies: 1
Views: 2264

ERROR in Cingular Pole Projection 2 System call crashed

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...
by francois
Wed Jun 05, 2019 1:32 pm
Forum: BrainVISA
Topic: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database
Replies: 12
Views: 5448

Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

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...
by francois
Mon Mar 04, 2019 3:39 pm
Forum: BrainVISA
Topic: BrainVISA's python crashes after last Ubuntu16 upgrade
Replies: 4
Views: 3950

Re: BrainVISA's python crashes after last Ubuntu16 upgrade

Removing all these libraries fixed python.
Thanks!
by francois
Wed Feb 27, 2019 12:56 pm
Forum: BrainVISA
Topic: BrainVISA's python crashes after last Ubuntu16 upgrade
Replies: 4
Views: 3950

Re: BrainVISA's python crashes after last Ubuntu16 upgrade

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-...
by francois
Wed Feb 27, 2019 12:24 pm
Forum: BrainVISA
Topic: BrainVISA's python crashes after last Ubuntu16 upgrade
Replies: 4
Views: 3950

BrainVISA's python crashes after last Ubuntu16 upgrade

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...
by francois
Thu Jan 31, 2019 6:56 pm
Forum: BrainVISA
Topic: Modification of /python/brainvisa/shelltools.py when working on Windows shares
Replies: 1
Views: 2519

Modification of /python/brainvisa/shelltools.py when working on Windows shares

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...
by francois
Tue Nov 13, 2018 12:00 pm
Forum: BrainVISA
Topic: Error with process Import_FROM_FreeSurfer_TO_Morpho.py
Replies: 6
Views: 4033

Re: Error with process Import_FROM_FreeSurfer_TO_Morpho.py

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...
by francois
Mon Nov 12, 2018 12:46 pm
Forum: BrainVISA
Topic: Error with process Import_FROM_FreeSurfer_TO_Morpho.py
Replies: 6
Views: 4033

Re: Error with process Import_FROM_FreeSurfer_TO_Morpho.py

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.
by francois
Fri Nov 09, 2018 5:33 pm
Forum: BrainVISA
Topic: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database
Replies: 12
Views: 5448

Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

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...
by francois
Fri Nov 09, 2018 4:30 pm
Forum: BrainVISA
Topic: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database
Replies: 12
Views: 5448

Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

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...
by francois
Fri Nov 09, 2018 3:01 pm
Forum: BrainVISA
Topic: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database
Replies: 12
Views: 5448

Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

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', )]) ...
by francois
Fri Nov 09, 2018 2:58 pm
Forum: BrainVISA
Topic: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database
Replies: 12
Views: 5448

Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

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 ...
by francois
Fri Nov 09, 2018 2:19 pm
Forum: BrainVISA
Topic: Error with process Import_FROM_FreeSurfer_TO_Morpho.py
Replies: 6
Views: 4033

Re: Error with process Import_FROM_FreeSurfer_TO_Morpho.py

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.
by francois
Thu Nov 01, 2018 1:10 pm
Forum: BrainVISA
Topic: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database
Replies: 12
Views: 5448

Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

Here is the complete sequence of error messages I get with the first execution of the FreeSurfer=>Morphologist process. It starts with a warning saying that the UUID of the nobias volume had to be changed (while this file didn't exist previously in the DB): Launch T1BiasCorrection Warning: changed u...
by francois
Thu Nov 01, 2018 11:20 am
Forum: BrainVISA
Topic: Error with process Import_FROM_FreeSurfer_TO_Morpho.py
Replies: 6
Views: 4033

Error with process Import_FROM_FreeSurfer_TO_Morpho.py

Any clue where is this error coming from? progress: 83.5714285714 / 100 ... Building left hemisphere attributed relational sulci graph... Traceback (most recent call last): File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/bin/real-bin/AimsFoldsGraphThickness.py", line 8...

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