ROI points representing intracranial electrode positions

Questions about Anatomist manipulation

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mheers
Posts: 10
Joined: Sat May 15, 2010 10:20 am

ROI points representing intracranial electrode positions

Postby mheers » Wed May 07, 2014 3:34 pm

Dear all,

I am trying to plot ROI points of intracranial EEG contacts in BrainVISA together with a brainsurface mesh. The segmented brainsurface is extracted from a MRI that was normalized to the MNI standard brain and I have the MNI coordinates of all implanted electrode contacts.

Is there a simple way to display both, the intracranial EEG contacts and the brainsurface in Anatomist?

Thanks a lot for your help!

Marcel

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riviere
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Re: ROI points representing intracranial electrode positions

Postby riviere » Wed May 07, 2014 4:38 pm

Hi,
Yes sure you can, in different ways.
You can represent the EEG contacts either using a ROI volume (or graph) in the same space as the subject MRI, or as small mesh objects (spheres for instance).
You can build small standard meshes using the AimsMeshGenerate command, which uses as input a small parameters file. For instance to build a sphere, write a parameters file (say we name it "params"):

Code: Select all

attributes = {
  'type': 'sphere',
  'center': [45.3, 72.6, 36.2],
  'radius': 1.,
  'facets': 50,
}

then using the command:

Code: Select all

AimsMeshGenerate -i params -o sphere.gii

Now you have to manage the coordinates transformations. If center coordinates are specified in the MNI space, it has to be specified for anatomist. This can be specified in the .minf file going with the mesh file (sphere.gii.minf):

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attributes = {
    'referential': '803552a6-ac4d-491d-99f5-b938392b674b',
    'material': {'front_face': 'counterclockwise'},
}

(the first line assigns the ID of the MNI referential in Anatomist to the mesh object, the second one tells about the triangles convention which is not the normal one in this direct referential).
Then you have to apply header transformation information to all objects (meshes and MRI) in anatomist (popup menu referentials/apply header informaton), provided the MRI has the correct transformation information to the MNI referential. If not, you will have to do it manually: see http://brainvisa.info/doc/anatomist/anatomist_referentials.pdf, or http://brainvisa.info/doc/aimsdata/aims_training/en/html/ch06.html.

You can of course script all of this, especially using Pyaims and Pyanatomist.

Denis


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