Search found 1348 matches

by riviere
Wed Oct 31, 2018 7:08 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: 6824

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

Hi, (it would probably better to use several topics for several problems, here the answers will not be clear). For now I only answer to the 1st problem. The problem occurs when re-inserting or updating a file in the database when it has already been inserted. Normally the system should check and upd...
by riviere
Fri Oct 26, 2018 6:31 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: 6824

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

Hi, That's right we have been observing this for a while, and have not found the cause yet (I must admit we have not searched very thoroughly). It isn't very harmful but the database has to be updated from time to time. I have put here a modified version of the database module which should print mor...
by riviere
Wed Oct 24, 2018 9:47 am
Forum: Anatomist
Topic: Displaying FreeSurfer aparc.a2009s+aseg atlas with correct colors
Replies: 2
Views: 3787

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

Hi François, The min/max you see in the interface are the min/max values of the image voxels (aparc.a2009s+aseg.mgz), not the palette. At the beginning palettes were meant to have an arbitrary number of colors, which are linearly mapped to the interval of the voxel image values. In this situation th...
by riviere
Wed Oct 24, 2018 9:03 am
Forum: BrainVISA
Topic: Problem Downloading from http://brainvisa.info/web/download.html
Replies: 1
Views: 2683

Re: Problem Downloading from http://brainvisa.info/web/download.html

Hi,
Oh you are right, a link to the download directory has been erroneously removed on the web server. I think it is OK now.
Denis
by riviere
Mon Oct 22, 2018 9:46 am
Forum: BrainVISA
Topic: BrainVisa Suite installation error
Replies: 5
Views: 4308

Re: BrainVisa Suite installation error

Hi,
Yes, there was the same issue on different systems, I have made some fixes (on Ubuntu 16, Mac, Windows 32/64, Mandriva), I didn't take time to test all of them but as it was the same problem, I hope they are fixed now. Tell us...
Denis
by riviere
Mon Oct 15, 2018 3:59 pm
Forum: BrainVISA
Topic: BrainVisa Suite installation error
Replies: 5
Views: 4308

Re: BrainVisa Suite installation error

Hi, Yes you are right the Ubuntu 16.04 version had broken dependencies. I don't really know how this got messed up (I did a manual fix afterwards and I must have done something wrong). I have rebuilt the entire packages so I hope it is better now. The thing is I can't remember why I did this manual ...
by riviere
Sat Oct 06, 2018 4:09 pm
Forum: BrainVISA
Topic: bvproc : parameter is not readable or does not exist ERROR
Replies: 2
Views: 3069

Re: bvproc : parameter is not readable or does not exist ERROR

Hi, There was probably a problem of access right on the attachments directory on our server. I have changed it, I hope it works better but I haven't tested it. What kind of normalization have you configured in brainvisa (SPM, FSL...), and which one is selected in your pipeline ? Depending on it the ...
by riviere
Sat Oct 06, 2018 3:54 pm
Forum: BrainVISA
Topic: KeyError while running Morphologist on command line
Replies: 9
Views: 5927

Re: KeyError while running Morphologist on command line

Hi Durai, When I copy/paste the commandline to try it I don't get exactly the same error, but I get a different one (however I'm not using version 4.6.0, I am using the bugfix branch of the sources): ValueError: invalid literal for int() with base 10: 'true' This is due the the boolean value of &quo...
by riviere
Tue Sep 25, 2018 6:28 pm
Forum: BrainVISA
Topic: New update 4.6.1 of BrainVisa
Replies: 0
Views: 7731

New update 4.6.1 of BrainVisa

A new update 4.6.1 of BrainVisa / Anatomist is available.
It contains mainly bug fixes (and should fix the Mac version we hope).
See the changelog for more information.
Or go to the download section to try it.
by riviere
Fri Sep 07, 2018 2:57 pm
Forum: AIMS
Topic: Difference of behavior in cutMesh
Replies: 5
Views: 10038

Re: Difference of behavior in cutMesh

I have fixed the problem but you will need a new compiled package. I'll do that next week. Otherwise the forum notification seems to be broken, I also don't receive any email when new posts or answers are in the forum. I don't know why, and I'm afraid I really have no time to investigate right now. ...
by riviere
Thu Sep 06, 2018 4:42 pm
Forum: AIMS
Topic: Difference of behavior in cutMesh
Replies: 5
Views: 10038

Re: Difference of behavior in cutMesh

Hi François,
I get the same behavior so I can reproduce the problem. It's obviously a bug, probably in the way the function is called since the algorithm has not changed and is still working inside anatomist. I'll investigate.
Denis
by riviere
Wed Aug 15, 2018 9:18 pm
Forum: Anatomist
Topic: save an image of the colormap like a colorbar in matlab/matplotlib
Replies: 1
Views: 2941

Re: save an image of the colormap like a colorbar in matlab/matplotlib

Hi Guillaume, Sorry I didn't see your post, the forum notification seems broken... Palette images are all images in jpeg, png, or ima formats, but I guess what you want is the colormaps with scale factors applied, and associated image or texture values, right ? Well, there is nothing builtin for tha...
by riviere
Wed Aug 15, 2018 9:08 pm
Forum: BrainVISA
Topic: Holes in white matter mesh
Replies: 1
Views: 2971

Re: Holes in white matter mesh

Hi Olivier, Sorry I didn't see your post, the forum notification seems broken... Well, what you're saying is a bit frightening... If the decimation process creates holes in meshes, it's not normal at all. The algorithm hasn't been modified in decades so all meshes ever created by brainvisa might be ...
by riviere
Thu Jul 12, 2018 3:12 pm
Forum: Anatomist
Topic: RGBA palette in pyanatomist
Replies: 6
Views: 4355

Re: RGBA palette in pyanatomist

Right ;)
By the way I fixed the update bug in anatomist sources (bug_fix branch, version 4.6.1).
Denis
by riviere
Tue Jul 10, 2018 2:49 pm
Forum: BrainVISA
Topic: Errors with Sulci Recognition in Morphologist Pipeline
Replies: 2
Views: 3283

Re: Errors with Sulci Recognition in Morphologist Pipeline

Hi Will, Sorry I missed the notificatioin for your message and I had not seen it before today... Well... First the Mac version is definitely not optimal: we use an old Mac system (10.5) featuring an old compiler, an old python language version, and old libraries. We have seen that some programs run ...

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