Search found 63 matches

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: 25190

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: 18632

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...
by francois
Thu Nov 01, 2018 11:14 am
Forum: BrainVISA
Topic: Error message: htmllib.HTMLParseError: unexpected call to parse_starttag
Replies: 1
Views: 11858

Error message: htmllib.HTMLParseError: unexpected call to parse_starttag

I get a lot this error. It looks like an error in the error message display rather than in the process in itself. I suspect I miss some more interesting error messages because of this. How can I fix this? Launch VipGreyStatFromClassif to generate a histo analysis file Now run the last part of the re...
by francois
Tue Oct 30, 2018 8:46 am
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: 25190

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

And a third blocking issue I get with the process Import_FROM_FreeSurfer_TO_Morpho.py . Sometimes it works, sometimes not... what am I doing wrong? progress: 83.5714285714 / 100 ... Building left hemisphere attributed relational sulci graph... Traceback (most recent call last): File "/home/ftad...
by francois
Tue Oct 30, 2018 8:41 am
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: 25190

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

In the same context, I also have this other error regularly: Launch VipGreyStatFromClassif to generate a histo analysis file Now run the last part of the regular Morphologist pipeline. SkipSkip unselected unselected node: Image orientation handlingnode: progress: Image orientation handling 0.0 / 100...
by francois
Tue Oct 30, 2018 8:24 am
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: 25190

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

Now I get this: Launch T1BiasCorrection UUID conflict in database, uuid: 3f4fea27-3899-ddcc-b9ad-b9a83f3a1dbd error: UNIQUE constraint failed: _DISKITEMS_._uuid while inserting: /home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0001BAR_FreeSurfer/t1mri/FreesurferAtlaspre_2016-11-27/default_analysis/nobias...
by francois
Thu Oct 25, 2018 7:33 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: 25190

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

Hello, I'm having this issue when trying to run Morphologist on a FreeSurfer segmentation. How is this possible that two files get attributed exactly the same UUID? How can I know which is the offending file, and what can I do to get around this issue? Thanks Francois Process Import FreeSurfer grey/...
by francois
Wed Oct 24, 2018 10:03 am
Forum: Anatomist
Topic: Displaying FreeSurfer aparc.a2009s+aseg atlas with correct colors
Replies: 2
Views: 12747

Re: Displaying FreeSurfer aparc.a2009s+aseg atlas with correct colors

Great, it works!
I tried with maxVal=the number of colors, but without this option "absoluteMode".
Thanks!
by francois
Tue Oct 23, 2018 6:44 pm
Forum: Anatomist
Topic: Displaying FreeSurfer aparc.a2009s+aseg atlas with correct colors
Replies: 2
Views: 12747

Displaying FreeSurfer aparc.a2009s+aseg atlas with correct colors

Hello I'm trying to display the FreeSurfer Destrieux atlas (aparc.a2009s+aseg.mgz) in Anatomist, with appropriate colors: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT The voxel values in this atlas go from 0 to 14175. To display the atlas correctly in anatomi...
by francois
Fri Sep 07, 2018 3:43 pm
Forum: AIMS
Topic: Difference of behavior in cutMesh
Replies: 5
Views: 32609

Re: Difference of behavior in cutMesh

Ok thanks!
I'll wait for your update instead of trying to recode cutMesh on my end then.
(I will need both the Ubuntu16 and Mandriva2008 versions... sorry for the added work)
by francois
Fri Sep 07, 2018 2:37 pm
Forum: AIMS
Topic: Difference of behavior in cutMesh
Replies: 5
Views: 32609

Re: Difference of behavior in cutMesh

Thanks Btw, I am "subscribed" to the topic but I don't receive the new posts by email. I checked the preferences of my account and it all seems to indicate that I should receive notifications by email. So I just keep the page open and refresh it from time to time... Is there anything I'm n...
by francois
Wed Sep 05, 2018 1:52 pm
Forum: AIMS
Topic: Difference of behavior in cutMesh
Replies: 5
Views: 32609

Re: Difference of behavior in cutMesh

Any update on this topic?
Should I start looking for another solution?
by francois
Fri Aug 31, 2018 7:34 pm
Forum: AIMS
Topic: Difference of behavior in cutMesh
Replies: 5
Views: 32609

Difference of behavior in cutMesh

Hello, I noticed a weird difference of behavior between the stable 4.6.0 and a recent 4.6.1 build that Denis sent me (Ubuntu16). Consider the following code: mesh = aims.read("/home/ftadel/test_cutmesh/test_mesh.gii") testcut = aims.AimsSurfaceTriangle() border = aims.AimsTimeSurface(2) ai...
by francois
Mon May 28, 2018 2:40 pm
Forum: Anatomist
Topic: Registration issue
Replies: 3
Views: 11873

Re: Registration issue

It looks like it's working when I do it when starting anatomist from the command line. But I haven't managed to make it work yet when starting anatomist from a python script. These two preferences to change are not saved from one session to the next. How do I set this programmatically? (after callin...
by francois
Mon May 28, 2018 11:37 am
Forum: Anatomist
Topic: Registration issue
Replies: 3
Views: 11873

Registration issue

Hello, I have a non-isotropic volume (t1pre.nii) that I have processed with FreeSurfer. I have imported the FreeSurfer output back to my BrainVISA database with the "Freesurfer outputs To BrainVisa conversion pipeline". I want to display the FreeSurfer/MarsAtlas parcellation together with ...