fusion of functional 3D map with inflated cortex

Questions about Anatomist manipulation

Moderators: denghien, riviere

Post Reply
SylvainT
Posts: 73
Joined: Mon Feb 13, 2006 6:37 pm
Location: INT, Marseille, France

fusion of functional 3D map with inflated cortex

Post by SylvainT »

hi all!

I'm trying to create an overlay of a statistical map coming from SPM onto an inflated cortex. I was told that I need to do a first fusion to then export a texture, and then redo a fusion with the texture, but I'm not 100% sure about all this, and the values I get in the texture (according to what I can see with the color palette) seem to be different from the original stat maps, so I think I'm doing something wrong somewhere... what I'd like to do, is threshold the textured statistical map with a given threshold (F=3.4 for example) on my final overlay, using the palette control.

is there a tutorial somewhere explaining how to do this properly? if not, could you please guide me step by step?

thanks,

sylvain
User avatar
riviere
Site Admin
Posts: 1361
Joined: Tue Jan 06, 2004 12:21 pm
Location: CEA NeuroSpin, Saint Aubin, France
Contact:

Post by riviere »

Hi,

Yes, you have to do 2 fusions, but you don't need to export a texture anymore :
- do one Fusion3D between the statistical map (volume) and the regular mesh, to make an object which has a texture corresponding to the intersection of the mesh on the volume. You can change the fusion settings to select how the interpolation is done
- do a TexturedSurface between the inflated mesh (which must have the same structure as the first mesh: same number of vertices and same ordering) and the previous Fusion3D object, to apply the Fusion3D texture to the inflated mesh.

I don't think this is documented anywhere, but the "fusion" principle is general enough to allow many combinations (I mean, this specific type of double-fusion wasn't meant in Anatomist program: there is no specific code for this inflated brain case, but it happens that we can do it using the general fusion system, and I discovered that we could use it for this purpose afterwards). Just experiment, you'll maybe discover some combinations nobody has ever thought about...

Denis
SylvainT
Posts: 73
Joined: Mon Feb 13, 2006 6:37 pm
Location: INT, Marseille, France

Post by SylvainT »

thanks denis, I finally gave this a try and it works smoothly ;)
julianm
Posts: 1
Joined: Thu Mar 01, 2007 2:20 pm

Post by julianm »

Hi,
I am trying to do exact the same thing, however because I just installed BrainVisa I am very unfamiliar with the interface. And it doesn't really help with a french manual.

All I want to do with this software is to display my SPM parametric maps on an inflated brain.

Could someone give me the step by step "dummy" aproach for this? I would be very greatful

//Julian
riviere wrote:Hi,

Yes, you have to do 2 fusions, but you don't need to export a texture anymore :
- do one Fusion3D between the statistical map (volume) and the regular mesh, to make an object which has a texture corresponding to the intersection of the mesh on the volume. You can change the fusion settings to select how the interpolation is done
- do a TexturedSurface between the inflated mesh (which must have the same structure as the first mesh: same number of vertices and same ordering) and the previous Fusion3D object, to apply the Fusion3D texture to the inflated mesh.

I don't think this is documented anywhere, but the "fusion" principle is general enough to allow many combinations (I mean, this specific type of double-fusion wasn't meant in Anatomist program: there is no specific code for this inflated brain case, but it happens that we can do it using the general fusion system, and I discovered that we could use it for this purpose afterwards). Just experiment, you'll maybe discover some combinations nobody has ever thought about...

Denis
User avatar
Olivier Coulon
Posts: 176
Joined: Fri Feb 27, 2004 11:48 am
Location: MeCA research group, Institut de Neurosciences de La Timone, Marseille, France
Contact:

Post by Olivier Coulon »

Julian,
the first thing to do is to sort out the language thing. Go to the preference menu, "general" section, and chose english in the language box, then restart brainvisa. It opens with a "brainvisa help" page in the right pane. You should start from there. For your particular purpose , and after you read the help pages, you should import your data in the Brainvisa database, then run the anatomical pipeline up to the mesh creation. Then run the "anatomy->T1 Pipeline 2004->triangulation->Ana Inflate Cortical Surface" process on the grey/white interface mesh.
let us know if you meet any problem on the way.

Olivier
Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
denghien
Posts: 209
Joined: Mon Apr 05, 2004 1:35 pm
Location: IFR49 / SHFJ Orsay
Contact:

Post by denghien »

Hi,

I have written an english training documentation. There are basic and advanced levels. Do you want to try it to start with Anatomist and could you give me your opinion before we will propose on the web site ?

Isa
User avatar
Olivier Coulon
Posts: 176
Joined: Fri Feb 27, 2004 11:48 am
Location: MeCA research group, Institut de Neurosciences de La Timone, Marseille, France
Contact:

Post by Olivier Coulon »

Do you want to try it to start with Anatomist and could you give me your opinion before we will propose on the web site ?
Yes, I'll be very happy to do that.

Olivier
Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
denghien
Posts: 209
Joined: Mon Apr 05, 2004 1:35 pm
Location: IFR49 / SHFJ Orsay
Contact:

Post by denghien »

Ok :)
I know your email. I'm going to send you the training book.
Isa
Post Reply