Problem to read volume

Questions about Anatomist manipulation

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maruko
Posts: 9
Joined: Mon Jun 11, 2007 9:38 pm

Problem to read volume

Post by maruko »

I can read an mri volume with brainvisa (anatomist), i have only the axes!!

Sorry for my english, can i ask my question in french? :oops:
denghien
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Post by denghien »

Hi,

No in english is good but I need more details about your problem.

I have an idea, when you say " i have only the axes", I suppose you see only the linker cursor in a window of Anatomist. I supppose that your volume is not in the correct type of window. In fact in order to view a 3D volume, you must use axial, coronal or sagittal window and not a 3D window (pyramid icon). If you place a 3D volume in a 3D window is not completely wrong because the volume is in a particular plane and you must move the volume by using the middle button of your mouse to rotate the volume of this window.

In order to view a volume with Anatomist, please work as follows:
- File => Open.
- Select your object with the file browser
- This object appears in the left list of the control window.
- Open an axial window by clicking on axial window (on left).
- Put the object (the volume) into this window: drag and drop this object into the window.

You can launch Anatomist and Brainvisa on your workstation ?
Which kind of OS ? Linux ? Windows ?

Isa
maruko
Posts: 9
Joined: Mon Jun 11, 2007 9:38 pm

Post by maruko »

Hello,
Sorry for my late response!
i' ve used an axial, coronal and sagittal windows to view the volume, and have only the axes.
When i use brainvisa, it call anatomist when i click on the icone (eye), and i have the same problem (the axis only).
i have another question, can i read the volume (.ima) with another application (spm matlab), how can i change the format from .ima to .img?.

My OS is windows Xp
Thanks in advance
denghien
Posts: 209
Joined: Mon Apr 05, 2004 1:35 pm
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Post by denghien »

Hi,

It is strange. Could you tell me what is the graphic card (Nvidia, chipset, ATI ...) ? And could you send me a snpashot of "the axis" and the volume that you want to visualize ?
Send me a private mail to give you a ftp adress.

To view .ima with an other soft, data must be converted.
In order to convert, you can use the following brainvisa process:
- set the user level to "advanced" in "Preferences -> General"
- use the "Converters -> automatic -> AimsConverters" process


Isa
maruko
Posts: 9
Joined: Mon Jun 11, 2007 9:38 pm

Post by maruko »

hi,
i dont think that my graphic card is the problem, i can visualise the volume with other application (mricro,spm)...etc.
I have downloaded the image from Brainweb, and i used vipbiascorrection and convert the images to visualise it with mricro.
I dont know what is the problem when i try to visualise the volume with anatomist
denghien
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Post by denghien »

Hi,

I think Anatomist doesn't work like spm or mricro because OpenGL is used by Anatomist to improve the graphic performances. So it's important to known which is your graphic card.

Could you send me a snpashot of "the axis" and the volume that you want to visualize ? Otherwise it is difficult to unterstand what is happened.

To obtain other demonstration data and tutorial, you can download the 'demo_data_td_2007.zip' of the section 'Exemple Data' on http://www.brainvisa.info/downloadpage.html .

Send me a private mail today because I'm going to go on holiday until the Monday 27 August.


Isa
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riviere
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Post by riviere »

Hi,

Isa is right, I just want to add a precision: anatomist uses OpenGL to render everything (volumes, meshes and so on), and also uses some "uncommon" OpenGL features (understand: features not used in games, like shared objects rendered across multiple windows). Some 3D drivers and OpenGL implementation are known to be buggy, especially on machines with Intel 3D chipsets. So it may actually be the cause of the problem, even if other software display things correctly.
On Intel chipsets, a classical trick to get it work is to lower the hardware 3D acceleration on windows.

Denis
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