How to add the egde for the mask

AFNI Message Board
1

I create a mask as ROI, now I want to add the edge for the mask. How can I do it?

2

Hi-

I don’t quite understand. Can you provide a bit more description? It is correct that you have a volume with a single ROI in it, and you just the edge of it?

There are different ways to do so; there is also some decision-making about what is meant by “edge”: are the voxels connected by any of voxel-faces or -nodes or -edges, or a subset of those? There are also various permutations depending on whether you have multiple ROIs per voxel (it sounds like that is not the case here).

The way I would start by doing this would be to calculate the depth of the ROI in terms of voxel counts:


3dDepthMap \
    -zeros_are_zero \
    -ignore_voxdims \
    -prefix mask_depth.nii.gz \
    -input DSET_ROI

… and then use the following 3dcalc command to find nonzero places in the depth map below a certain value—using 1.2 here will keep a boundary connected by voxel-faces or voxel-edges:


3dcalc \
    -a mask_depth.nii.gz \
    -expr 'bool(a)*step(1.2-a)' \
    -prefix mask_edge.nii.gz \
    -overwrite

Those images are attached, showing the ROI as underlay, first with the depth calculation and then with the boundary calculation.

–pt

img_depth.jpg

img_boundary.jpg

3

Hi，
Thank you so much for your reply. Actually, I created some masks as my ROI. And I give the masks different values. Then I use 3dcalc to compose these masks.like:3dcalc -a AN.nii -b VN.nii -c DMN.nii -d ECN.nii -expr ‘a+b+c+d’ -prefix Network.nii. The final result is the first picture.
Now what I want to do is add the edges for the mask. Then I will use SUMA to get a surface. So I want to add the edges to make the boundary between ROI clearer, like the second picture.

4

Paul has some cool solutions for showing edges in the volume, but you may be interested in showing contours on surface maps as described in this previous post:

https://afni.nimh.nih.gov/afni/community/board/read.php?1,167734,167743#msg-167743