Old pipeline and issue with BrainVisa

Questions about BrainVisa usage and installation

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Maxim3
Posts: 3
Joined: Sat Mar 22, 2014 3:48 pm

Old pipeline and issue with BrainVisa

Post by Maxim3 »

Dear all,

Thanks for reading this.
I want to perform sulci analyses and have some trouble. I follow a step by step method from a colleague of mine (I need to follow it in order to have the same procedure for our common data), which requires to use Morphologist 2012 to have 3.0 graph and then to use an old composant "mise à jour des plis corticaux" to convert the 3.0 graph that I obtained into a 3.1.

1 - Mac
I use the 4.4.0 version of BrainVisa in expert mode (to have the old stuff) on Mac Os X Lion 10.7.5.

I succeed in having the 3.0 graph and in converting it in 3.1, but when I want to use the "statistiques morphométriques", I have some trouble with the "Labels Selector" tool (in clicking on "...") after to have imported the "Left cortical fold" (or the right) in 3.1. I need this tool because we have some ROI to make with it. Unfortunately, the "Labels Selector" is opening fine, but 2 sec after, it is not respond anymore (it's freezing) and I have to force the close.

I don't know what to do and think I've tried everything : import the "Labelled Left Cortical Fold" file as well, but the Labels Selector does not work.

2 - Windows
I use the 4.2.1 (and have tried with the 4.1) version of BrainVisa in expert mode as well, on Windows Xp SP3.

This time, I have some trouble very early in the analyses : when I tried to import T1 MRI.

Actually, when I try to create a database, BrainVisa tells me that "u C:/database has no uuid", and consecutively, I can't specified any output during the importation of T1 images. I tried to reinstall BrainVisa several time (with successive versions), and before this, I also have consistently deleted the .brainvisa folder in the home folder of Windows (Documents and setting/Application data/.brainvisa) and did a research on recently added files to delete any temporary files created by BrainVisa.
I also I've tried to rename the option.minf in option.minf.bak before to create the database.
But nothing worked and I can specified any output...

Well, I can go any further, and I crucially need your help please.
Thank you very much,
Maxime.
Maxim3
Posts: 3
Joined: Sat Mar 22, 2014 3:48 pm

Re: Old pipeline and issue with BrainVisa

Post by Maxim3 »

Hello here,

I have tried to perform a sulci analyses with the new BrainVisa (4.4.0) and the new Morphologist (2013) on my Mac (10.7.5).
So I've pretty much done nothing except download and install SPAM and follow the Morphologist pipeline, with Talairach and Labelisation activated.
This time, everything was perfect and quick.

But when I've tried to use the Label selectors, it freezed again and I have to force it to quit with Os X.
So even with the new tools, I cannot use the label selectors.

Could you help me on this please ?
Thank you.
Maxime.
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riviere
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Joined: Tue Jan 06, 2004 12:21 pm
Location: CEA NeuroSpin, Saint Aubin, France
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Re: Old pipeline and issue with BrainVisa

Post by riviere »

Hi,

I must admit that graphical tools are not thoroughly tested on Mac and Windows: we are developing on Linux, and have some (a few...) automatic tests for processing results, but cannot automatically test every interactive graphical tool, so it is possible that some of them are not working properly on all systems.
I will have a look at it when I get time (next week probably) but I can only test on MacOS 10.5. So I'll tell you if I get the same problem.

Denis
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riviere
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Re: Old pipeline and issue with BrainVisa

Post by riviere »

Hi,
Sorry for the late answer...
There was a bug in AimsLabelSelector in the release 4.4.0 (a Qt event loop problem). It has been fixed since but we had not provided an update for it (and I just forgot about it then...). The problem was here on all systems actually, not only Mac and Windows.
I just did it: you can download it from ftp://ftp.cea.fr/pub/dsv/anatomist/updates/4.4.0
For each system, the updated executable is at the same directory tree location as in the regular BrainVisa install. You can replace the one from your brainvisa install with the one found there.
Denis
Maxim3
Posts: 3
Joined: Sat Mar 22, 2014 3:48 pm

Re: Old pipeline and issue with BrainVisa

Post by Maxim3 »

Hi and thank you for your help Denis...

Unfortunately, when using this new version, the label selector window does not open when I click on the "..." near the region parameter in the Morphometric statistics.
Nothing happen and I cannot select my regions...

Any ideas please ?
Thank you again,
Maxime.
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