Search found 176 matches

by Olivier Coulon
Mon Feb 19, 2018 5:01 pm
Forum: BrainRAT toolbox
Topic: Primatologist crash due to sql problem
Replies: 2
Views: 3076

Re: Primatologist crash due to sql problem

Thank you for your answer, Denis, it did fix the problem.
I tried on my Ubuntu machine.
I will try on the Debian, if it does not work I'll let you know but I don't see why not.

Olivier
by Olivier Coulon
Wed Feb 14, 2018 3:50 pm
Forum: BrainRAT toolbox
Topic: Primatologist crash due to sql problem
Replies: 2
Views: 3076

Primatologist crash due to sql problem

Hello, although my question is related to the new Primatologist toolbox, I am asking it here because Primatologist comes with BrainRat. Let me know if you want me to post it on the BrainVsa forum. So I have installed Brainvisa 4.6 on an Ubuntu14.04 machine, as well as on a Debian machine. I tried th...
by Olivier Coulon
Mon Jul 10, 2017 5:36 pm
Forum: BrainVISA
Topic: Freesurfer is not identified in BrainVISA
Replies: 15
Views: 10006

Re: Freesurfer is not identified in BrainVISA

Hello Denis,
what is the use of the renormalization process. I am asking because several collaborators encountered the problem. Your patch solves it but I am thinking about the consequences of using AimsMIRegister if the process that is not very robust.
Thanks,
Olivier
by Olivier Coulon
Fri Jun 30, 2017 12:46 pm
Forum: BrainVISA
Topic: BrainVISA crashes while doing the Sulcus Parameterization2015 in iteration mode
Replies: 10
Views: 6642

Re: BrainVISA crashes while doing the Sulcus Parameterization2015 in iteration mode

Hello, concerning this issue: Sulcus Parameterization 2015 has a bug that causes the program to use the same ouput file names over and over again without adding some subject identifier (after the iteration process you only have ouputs for 1 subject no matter how many iteration processes were made). ...
by Olivier Coulon
Mon Jun 26, 2017 2:40 pm
Forum: BrainVISA
Topic: Morphologist : how to normalize native lengths?
Replies: 2
Views: 3542

Re: Morphologist : how to normalize native lengths?

Hello, I am not sure that the question was about normalizing a distance afterwards with a spatial normalization transformation. One would think that it is possible for instance to normalize distance-related measurements with a length related to brain size... (e.g. largest euclidean distance between ...
by Olivier Coulon
Mon Jun 19, 2017 8:26 am
Forum: BrainVISA
Topic: BrainVISA crashes while doing the Sulcus Parameterization2015 in iteration mode
Replies: 10
Views: 6642

Re: BrainVISA crashes while doing the Sulcus Parameterization2015 in iteration mode

Hello,
my guess is that the problem is unrelated to the process, it is more general. Would it be possible for you to try with the same data on another system (Linux or Mac) ?

Olivier
by Olivier Coulon
Wed Jun 14, 2017 11:21 am
Forum: BrainVISA
Topic: BrainVISA crashes while doing the Sulcus Parameterization2015 in iteration mode
Replies: 10
Views: 6642

Re: BrainVISA crashes while doing the Sulcus Parameterization2015 in iteration mode

Hello,
are you running all these subjects iteratively or in the 'run in parallel' mode ?

Olivier
by Olivier Coulon
Tue May 30, 2017 8:54 am
Forum: BrainVISA
Topic: Freesurfer is not identified in BrainVISA
Replies: 15
Views: 10006

Re: Freesurfer is not identified in BrainVISA

Hello, although the initial problem has been solved, I am sending a follow up because we seem to have an issue with the Freesurfer toolbox and FS6.0. Both laura and I encountered the same problem using FS6.0. The main FS pipeline is working fine but when using the 'Import FreeSurfer grey/white segme...
by Olivier Coulon
Wed May 24, 2017 3:23 pm
Forum: BrainVISA
Topic: Freesurfer is not identified in BrainVISA
Replies: 15
Views: 10006

Re: Freesurfer is not identified in BrainVISA

Great, I'm glad it works.

Olivier
by Olivier Coulon
Wed May 24, 2017 2:11 pm
Forum: BrainVISA
Topic: Freesurfer is not identified in BrainVISA
Replies: 15
Views: 10006

Re: Freesurfer is not identified in BrainVISA

Hello Laura, you wrote this: I usually run BrainVISA as sudo This might be the source of your problem. You don't need to run it with sudo. Just type: /usr/local/brainvisa/BrainVISA (if the install directory is not '/usr/local/brainvisa', change it accordingly, e.g. '/usr/local/brainvisa-4/5/0/BrainV...
by Olivier Coulon
Wed May 24, 2017 12:55 pm
Forum: BrainVISA
Topic: Freesurfer is not identified in BrainVISA
Replies: 15
Views: 10006

Re: Freesurfer is not identified in BrainVISA

Hello Denis, just to add some information: I exchanged a few emails with laura and it turns out that the .brainvisa/options.minf contains the freesurfer paths, so it is even stranger that they do not appear in the preferences. Also, about the freesurfer version: I am using FS 6.0 on a machine here a...
by Olivier Coulon
Tue Feb 14, 2017 6:24 pm
Forum: Anatomist
Topic: anatomist texture rendering no interpolation
Replies: 8
Views: 7033

Re: anatomist texture rendering no interpolation

Hello, I m sorry but I don't see the problem with the interpolation ? It is displayed as it should to me... Nevertheless, the MarsAtlas viewer is setup to display like this. You're only option to change the texture interpolation is, in the main Anatomist window, to right click on the mesh+texture fu...
by Olivier Coulon
Mon Oct 31, 2016 12:24 pm
Forum: BrainVISA
Topic: AimsSulcalLines
Replies: 4
Views: 5243

Re: AimsSulcalLines

OK, I'll see that with Arnaud Letroter and will come back to you.

Olivier
by Olivier Coulon
Mon Oct 31, 2016 11:30 am
Forum: BrainVISA
Topic: AimsSulcalLines
Replies: 4
Views: 5243

Re: AimsSulcalLines

Hello,
we found a bug in the AimsSulcalLine program, that we corrected nut you'll have to wait for the next bug_fix release to have the correction. It might be the origin of your problem. Is it an occasional problem or does it happen for all subjects ?

Olivier
by Olivier Coulon
Fri Jul 22, 2016 7:49 am
Forum: BrainVISA
Topic: Hip-Hop138 avg template
Replies: 2
Views: 2153

Re: Hip-Hop138 avg template

Hello, the template has been built with a sub part of the OASIS database. The same group has already been used in [Auzias et al., Neuroimage, 111:12-25, 2015]. In a nutshell: subjects are healthy, 18-34 years old, mean age 23 years old, equal number of men and women. I will add these details on the ...

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