How to make ROIs of different depth from the surface of the SC?

AFNI Message Board
1

Hi all,
I want to divide the superior colliculus (SC) into different layers according to the physical distance from each voxel in SC to the surface.That is,I want to make ROIs of different depth from the surface of the SC.The depth for each voxel in the SC will be calculated as the shortest distance from the voxel to all surface voxels.I would like to know if there are some other ways to make the ROIs except for manually drawing different layers?
Yu Zhang
Thank you!

2

Hi Yu Zhang,

Do you have FreeSurfer surfaces? If so, it would be easy to
create ROIs based on the distance from the inner node to the
outer node, for each node pair. That is not exactly the measure
of depth that you stated, but it could be a great starting point,
and you might even like that method.

  • rick
3

Hi Rick,

Thanks for your answers ! 

I have ROIs of the whole SC now. But I have no FreeSurfer surfaces and I want to finish creating ROIs of different depth in a short time.

So the solutions I can find are :
1.Draw the first layer (the surface layer or the 0 mm layer) of the SC ROI manually.
2.Calculate the shortest distance from the other voxels in the ROI of the whole SC to all voxels in the first layer.
3.Get the voxels (the other voxels in SC ROI except for the voxels in first layer ) with specific shortest distance out and combine these voxels into a new ROI. For example,the voxels with the distance of 0.5-1.5mm will be combined into a new ROI with the name of 1mm layer. Then I can make several ROIs of different depth (2mm,3mm,4mm) from the first layer of the SC.

However,I don’t know how to calculate physical distance from the voxels in the first layer to the other voxels in SC firstly.Secondly,I don’t know how to combine the voxels of the specific distance to a new ROI.