Search found 161 matches

by Dominique Geffroy
Thu Apr 19, 2012 2:47 pm
Forum: BrainVISA
Topic: runtime error in Split Brain Mask
Replies: 12
Views: 12767

Re: runtime error in Split Brain Mask

Hi, Did you look at the results of the previous steps to see where is the problem ? Did the bias correction and brain mask seem ok ? Are you sure you correctly specified the AC/PC points ? You could also try the last version of Morphologist which is named Morphologist 2012. It is included in Brainvi...
by Dominique Geffroy
Tue Apr 10, 2012 7:46 am
Forum: BrainVISA
Topic: gyral parcellation - Run in parallel
Replies: 2
Views: 4433

Re: gyral parcellation - Run in parallel

Hello, I'm affraid this process cannot be run in parallel for the moment. Indeed, it seems to try accessing the Brainvisa database whereas the databases features are disable in parallel run mode because because our database system cannot manage concurrent access. Maybe it is possible to change this ...
by Dominique Geffroy
Thu Mar 01, 2012 9:16 am
Forum: BrainVISA
Topic: brainvisa 4.2.1 Ubuntu 10.4
Replies: 6
Views: 8340

Re: brainvisa 4.2.1 Ubuntu 10.4

That's very strange. I've just tried the Linux 64 bits package on my Ubuntu 10.4 64 bits and I had no such problem. The error message is incomprehensible because the python in the package actually has a UserDict module with a IterableUserDict class in it... Could you check if you use the python and ...
by Dominique Geffroy
Wed Feb 29, 2012 2:31 pm
Forum: BrainVISA
Topic: brainvisa 4.2.1 Ubuntu 10.4
Replies: 6
Views: 8340

Re: brainvisa 4.2.1 Ubuntu 10.4

Which Brainvisa package did you install ? Linux or Linux 64 bits ?
by Dominique Geffroy
Wed Feb 29, 2012 2:22 pm
Forum: BrainVISA
Topic: brainvisa morphology extension
Replies: 7
Views: 10624

Re: brainvisa morphology extension

Ok, I see. I think you should ask Peter Kochunov directly. Maybe indeed, the extension is not yet compatible with Brainvisa 4.2.1 which is a very recent release.

Dominique
by Dominique Geffroy
Wed Feb 29, 2012 9:03 am
Forum: BrainVISA
Topic: 'Run in parallel' doesn't work for Import FS to T1 pipeline?
Replies: 3
Views: 5101

Re: 'Run in parallel' doesn't work for Import FS to T1 pipel

Hello, Indeed, I suppose it doesn't work because databases are deactivated when running processes in parallel because our current database system doesn't manage correctly concurrent access. So the importation part of the process, as it needs to use the database cannot be run in parallel. But it shou...
by Dominique Geffroy
Wed Feb 29, 2012 8:53 am
Forum: BrainVISA
Topic: brainvisa morphology extension
Replies: 7
Views: 10624

Re: brainvisa morphology extension

Hello,

What is the morphology extension and where did you download it ?

Dominique
by Dominique Geffroy
Wed Feb 29, 2012 8:50 am
Forum: BrainVISA
Topic: brainvisa 4.2.1 Ubuntu 10.4
Replies: 6
Views: 8340

Re: brainvisa 4.2.1 Ubuntu 10.4

Hello,

Did you modify your environment variables ?
What is the result if you type the command "which brainvisa" ?

Dominique
by Dominique Geffroy
Mon Feb 20, 2012 9:23 am
Forum: BrainVISA
Topic: BrainVISA / Anatomist 4.2.1
Replies: 1
Views: 5605

BrainVISA / Anatomist 4.2.1

The new release 4.2.1 of BrainVisa / Anatomist is available.
Important new features: easy parallel computing with Soma-workflow integrated in Brainvisa, a new Freesurfer toolbox, improved Morphologist pipeline...
See the changelog for more information.
Or go to the download section to try it.
by Dominique Geffroy
Wed Feb 08, 2012 12:29 pm
Forum: BrainVISA
Topic: How to cite BrainVISA ?
Replies: 0
Views: 39097

How to cite BrainVISA ?

If you want to talk about brainVISA as a framework, you can use the references listed here: http://brainvisa.info/doc/axon/en/help/aboutBrainVISA.html . But, as BrainVISA is hosting various toolboxes, you often need to cite also the research paper(s) describing the algorithm implemented in the toolb...
by Dominique Geffroy
Fri Jan 20, 2012 1:28 pm
Forum: BrainVISA
Topic: SPAM seems to be missing file
Replies: 4
Views: 6111

Re: SPAM seems to be missing file

I see. In fact, convert old databases processes should not be used on Brainvisa share database but only on user databases. Maybe I should limit the available choices in these processes parameters to avoid this problem.

Dominique
by Dominique Geffroy
Fri Jan 20, 2012 9:48 am
Forum: BrainVISA
Topic: SPAM seems to be missing file
Replies: 4
Views: 6111

Re: SPAM seems to be missing file

Hello, It is strange that some files of the brainvisa-share database have been moved to a trash directory. Did you use the process "Data Management -> Convert old database" or one the processes in "Data Management -> convert old database steps" on the brainvisa-share database ? A...
by Dominique Geffroy
Wed Jan 18, 2012 10:25 am
Forum: BrainVISA
Topic: Error for non-admin users - siGraph2Label
Replies: 1
Views: 3894

Re: Error for non-admin users - siGraph2Label

Hello, This warning means that the name of the .data directory indicated in the .arg (in the field filename_base) is not correct. In this case, a .data directory with the same name as the .arg will be search for. So if L[subject]_default_session_auto.data exists and is located in the same directory ...
by Dominique Geffroy
Tue Jan 17, 2012 4:50 pm
Forum: BrainVISA
Topic: Cortical Folds Graph -- 3.1 as default
Replies: 2
Views: 4989

Re: Cortical Folds Graph -- 3.1 as default

Hello, yes, you should also change the parameter links replacing in the function eNode.addLink... CorticalFoldsGraph_3_0.Lgraph by CorticalFoldsGraph_3_1.LeftCorticalFoldsGraph_3_1.graph and CorticalFoldsGraph_3_0.Rgraph by CorticalFoldsGraph_3_1.RightCorticalFoldsGraph_3_1.graph. Then it should wor...
by Dominique Geffroy
Tue Jan 03, 2012 2:25 pm
Forum: BrainVISA
Topic: Crash of Anatomist in ubuntu-10.04.3-desktop-i386
Replies: 1
Views: 3813

Re: Crash of Anatomist in ubuntu-10.04.3-desktop-i386

Hello, There are two things you can try: - Go to the preferences (menu settings -> preferences), in OpenGL tab, try to set 1 for the number of textures. Don't forget to save the preferences (menu settings -> preferences) - If it doesn't work, you can try to use software acceleration by copying the c...