Adding electrodes and dipoles in an anatomist scene

Questions about Anatomist manipulation

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grova
Posts: 10
Joined: Wed Mar 31, 2004 1:30 pm
Location: Montreal Neurological Institute

Adding electrodes and dipoles in an anatomist scene

Post by grova »

Hello ...

Just a litlle question to know if it exist some facilities in anatomist to create lines or arrows in a 3d scene ...

My objectif is to include EEG depth electrodes and EEG dipoles in a 3d scene shwing the anatomy.

Thanks in advance for your help

Christophe
***************************
Christophe Grova, PhD
PostDoc - EEG department
Montreal Neurological Institute, McGill University
email : christophe.grova@mail.mcgill.ca
tel : (514) 398 2184
fax : (514) 398 8106
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riviere
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Post by riviere »

Hi Christophe,

Right now there is no module in Anatomist to directly draw lines or arrows for electrodes, but there are a few other things that you can use as a starting point (in fact I'm not sure if you want to be able to manually draw electrodes or display the position of calculated sources):

- the ROI module allows to draw voxels, I think it doesn't exactly meets your needs but it's better than nothing and you can mesh the regions after they are drawn

- there is a Aims command to generate simple meshes (cylinders, arrows etc). If you want to display the localization and orientation of calculated sources, I think it is what you need. The command is AimsMeshGenerate, and the parameters file it uses is undocumented at the moment, but if you are interested I can write a little doc, or if you are courageous enough you can look at the sources in aimsdata: in src/aimsdata/mesh/surfacegen.cc

- and last, I know that Manik Bhattacharjee (LENA, Paris) is making a BrainVisa/Anatomist module to display and draw electrodes and paths, mainly for surgical planing of deep electrodes implantation. What you would like is maybe related to his work.

Denis
grova
Posts: 10
Joined: Wed Mar 31, 2004 1:30 pm
Location: Montreal Neurological Institute

Good idea !

Post by grova »

Hello Denis, I would be very interested in using AimsMeshGenerate to create cylinders and arrows .... if you could write a quick documention, or just show me an example to create an point, an arrow and a cylinder it would be great !!!

Thanks in advance

Christophe
***************************
Christophe Grova, PhD
PostDoc - EEG department
Montreal Neurological Institute, McGill University
email : christophe.grova@mail.mcgill.ca
tel : (514) 398 2184
fax : (514) 398 8106
***************************
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riviere
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Post by riviere »

The next version of AimsMeshGenerate will contain a documentation (when you use the -h option). Here is what it will output:

-i | --input <string>
input parameter file (.minf-like)
Possible types and parameters:

type : arrow
arrow_length_factor : relative length of the head
arrow_radius : radius of the tail
facets : (optional) number of facets of the cone section (default: 4)
point1 : 3D position of the head
point2 : 3D position of the center of the bottom
radius : radius of the head

type : cone
closed : (optional) if non-zero, make polygons for the cone end (default:
0)
facets : (optional) number of facets of the cone section (default: 4)
point1 : 3D position of the sharp end
point2 : 3D position of the center of the other end
radius : radius of the 2nd end
smooth : (optional) make smooth normals and shared vertices (default: 0)

type : cube
center : 3D position of the center
radius : half-length of the edge
smooth : (optional) make smooth normals and shared vertices (default: 0)

type : cylinder
closed : (optional) if non-zero, make polygons for the cylinder ends
(default: 0)
facets : (optional) number of facets of the cylinder section (default: 4)
point1 : 3D position of the center of the 1st end
point2 : 3D position of the center of the 2nd end
radius : radius of the 1st end
radius2 : (optional) radius of the 2nd end (default: same as radius)
smooth : (optional) make smooth normals and shared vertices (default: 0)

type : icosahedron
center : 3D position of the center
radius : radius

type : sphere
center : 3D position of the center, may also be specified as 'point1'
parameter
facets : (optional) number of facets of the cone section. May also be
specified as 'nfacets' parameter (default: 4)
radius : radius
smooth : (optional) make smooth normals and shared vertices (default: 0)

(I think the sphere shape was not in the stable version)

Denis
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