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Segmentation of Collarbone in CT - volume

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Alba on 29 May 2020
Commented: Alba on 2 Jun 2020
I'm new to matlab and my task is to segment the trachea (wind pipe) and the clavicle bones (Collarbones) in different CT volumes. I could finish the segmentation of trachea with success. In the second part, I could extract the entire set of bone within the volume and I have stuck at there. I couldn't extract both collarbones from the rest of bones. As I'm supposed to measue the lenght of at lease one of these bones, could you please enlight me on how to segment these two bones?
The bone extaction code I wote so far is,
load 3D_Configs.mat; % Load the Configs
% Get the folder path
folder = ('./Set_No_2');
d = dir(folder + "/*.dcm");
slice_location = [];
for k = 1:length(d)
info = dicominfo(folder + "/" + d(k).name);
slice_location(k) = info.SliceLocation;
% Read the DICOM volume
[V,sp] = dicomreadVolume(folder);
V = squeeze(V);
slice_location = sort(slice_location);
scale_factors = [sp.PixelSpacings(1,:) slice_location(2)-slice_location(1)]; % Rescale the volume based on the DICOM metadata
% Visualise the skeleton volume
vs = volshow(V,config,'ScaleFactors',scale_factors);
(I tried creating various volume masks with the help of Image Segmenter and tried to segment the collarbones. But all failed.)
(The "3D_Configs.mat" file is a config extract saved from the volumeViewer with cam angle. Attached here.).
The "Set_No_2" is the DICOM image folder.
Code developed to segment the trachea in 2D slices of DICOM images is also attached here.
Thanks a lot in advance.


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Answers (1)

Dinesh Yadav
Dinesh Yadav on 2 Jun 2020
Hi Alba,
I am aware of one method i.e when you know the location of points for the region of interest (i.e. collar bone) you can extract those points using imcrop3.
There are two more cropping methods randomCropWindow3d and centreCropWindow3d but using this will take trail and error if we dont know the co-ordinates of the region of interest.
Hope it helps.

  1 Comment

Alba on 2 Jun 2020
Thanks Dinesh. I'll try this and post an update.

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