Creating binary 3D mask from MR volume

46 次查看（过去 30 天）
banikr
banikr 2020-4-26
回答： banikr 2020-4-29
Hello All,
I am trying to create a 3D binary mask for MR head volume. The image has 0 intensity for background and the tissue inside the image has integers. Morphological operations provide me very noisy output.
This is after bwconncomp, thresholding and imerode options.
Are there better ways to get volumetric masks?
  8 个评论
显示 6更早的评论
Image Analyst
Image Analyst 2020-4-27
I don't think the noise on the mask is the issue. Why did your classification routine quit classifying stuff below that line other than the blue stuff? For some reason, you have a mask that just quits below that line, and that has nothing to do with little noisy blips on it.
banikr
banikr 2020-4-27
Yeah you are right, the noise has nothing to do with the classification.
The classification comes from CT image which only exists for the segmented section. Now for MR images there is no specific intensity scaling mechanism like CT. For my experiment, I also need the inferior section of the head labelled in MR space.
CT image was registered on MR space.

请先登录，再进行评论。

请先登录，再回答此问题。

回答（2 个）

Mrutyunjaya Hiremath
Hello banikr,
I think this is what you want ... if I am not wrong.
load mri;
% load mriVolume; %3D MRI data with data variable name 'mriVolume'
mriVolume = D;
% Assuming background pixels are 0
bwMask = false(size(mriVolume));
pixIndex = find(mriVolume > 0);
bwMask(pixIndex) = 1;
  3 个评论
显示 1更早的评论
Mrutyunjaya Hiremath
Mrutyunjaya Hiremath 2020-4-27
@ banikr,
ok got it, if MRI data is possible to share, please share. love to work on it.

请先登录，再进行评论。

banikr
banikr 2020-4-29
I just wanted to update the finding I have(following mask image).
I used the intensity 10 for thresholding and removed objects with area under 1000.
bi = (mr>10);
% volumeViewer(bi);
stat = regionprops(bi, 'Area', 'PixelIdxList');
for nn=1:length(stat)
s = stat(nn);
if s.Area<1000
continue;
end % remove small objects
bi = zeros(sz);
bi(s.PixelIdxList) = 1;
end
volumeViewer(bi);
I tried to explain the value 10.
J = mr(mr~=0);
>> SkinMusclePrc = prctile(J,[20, 100], 'all')
SkinMusclePrc =
2×1 int16 column vector
10
626
The value 10 is on 20 percentile of the distribution.
let me know if that helps your search also.

类别

在 Help Center 和 File Exchange 中查找有关 Image Segmentation 的更多信息

标签

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!

Translated by