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
Adding electrodes and dipoles in an anatomist scene
Adding electrodes and dipoles in an anatomist scene
***************************
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
***************************
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
***************************
- riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
- Location: CEA NeuroSpin, Saint Aubin, France
- Contact:
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
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
Good idea !
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
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
***************************
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
***************************
- riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
- Location: CEA NeuroSpin, Saint Aubin, France
- Contact:
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
-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