I am trying to search for a simple solution to this but haven’t come across anything yet…
I am trying to determine the surface area that is occupied by a certain number of vertices on a cortex surface. For example, if I have a source file with a bunch of vertices in a scout that have a value of 1 to 10 at a certain time sample, and I would like to know the area on the surface occupied by the color red of the colormap (= a value of 10), how would I go about calculating that?
I understand that vertices are points, and that the actual color on the source file is calculated with some kind of median filtering with nearby vertices, but my goal would be to create a script that would assign each vertex an area (e.g. 2mm^2) which would represent the area that this vertex’s value contributes to the colormap once the source file is displayed in Brainstorm. I could then use this “area” array in my other scripts to find the contribution of a certain value (e.g.10) on the cortex surface, in terms of area percentage/mm^2/other unit.
I hope I was clear enough! I feel like I should be using Faces or other data variables stored in the surface file, but I am not sure which one and what does each variable represent…
Thank you very much for any help!
You can use the Scout tab. When you select a scout, it shows at the bottom of the tab the number of vertices and an estimation of the area covered by this scout.
The area associated to each vertex is the sum of 1/3 of the area of each face it is contributing to.
Check the function tess_area.m, it does everything you need.
Do you mean: how to compute this vertex area values?
This is done by this function (check the code for more information):
[FaceArea, VertArea] = tess_area(sSurf)
What is the default threshold that brings BST to identify the active area in the estimation of source?
(I mean the red area by default in solving the inverse problem)
Do you know some criterion that indicates the threshold level for this type of matrix amplitude (ImageGridAmp)?
Do you have any physiological significance negative values in the array ImageGridAmp?
I have clear that the values of red or yellow colors are positive and higher compared to others, which are usually zero. However, I do not understand why there are negative values and unit pA / m, and which is a measure of the current density.
The default threshold is arbitrary (50% when you start brainstorm), this slider is there to allow you to display more or less values, to facilitate the interpretation of the maps.
For getting meaningful thresholds, you need to compute the significance of a difference, using t-tests for instance.
Alternatively, you can compute a Z-score normalization, this will give you values that are more meaningful than the current density values.
I’m returning to my study with head models.
Now, i’m trying to quantify the correct area from a inverse problem resolution.
being clear, i have my Gridamp with amplitude intensities for my model of (15002x150).
Then i extracted my area information from my model through the next code:
TEST = in_bst_data(sFiles.FileName);
export_matlab(TEST.SurfaceFile,‘x’);
[FaceArea, VertArea] = tess_area(x);
So i can save either (FaceArea and VertArea)
Then i’m taking a threshold like 50% from the vertex of highest intensity
from my Gridamp. So i will be able to relate Area, intensity and position.
my question is the next:
What i need to take the FaceArea or the VertArea info for to give a area quantification?
what is the unit to FaceArea and VertArea?
And finally my last question is , if i want to take the euclidean distance between 2 vertex:
In your surface “x”, you have two fields Vertices and Faces, to represent the mesh.
The function tess_area computes the area of each face (FaceArea(i) is the area of face Faces(i,:)).
To estimate the area attached to each vertex, we sum the area of all the faces that include the vertex and then divide by 3 (each face has three vertices).
VertArea(i) is the area of vertex Vertices(i,:).
All the values in Brainstorm files are in international units: meters (m) and squared meters (m2).