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how to display images from a nifti file?

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Emerson Nithiyaraj
Emerson Nithiyaraj on 4 Sep 2019
Commented: Manjunath R V on 29 Apr 2021
I have a liver CT dataset where all images is in .nii file format. Each image file has mulitple slices (say 512*512*500). Using niftiread command i read the image file and now I am visualizing each of the 500 slices one by one using imshow command.
imshow(i = Y(:,:,400)) %400 is my current slice number
Now my image 'i' is class int16 and has values from 0 to 2328. I think these values are Hounsfield units (HU). My image 'i' is like below, where i couldnt see any fine details from the image.
untitled.jpg
When i referred a paper they said as, 'the Hounsfield unit is applied in window range [100, 400] and then after some pre-processing steps the image is visualized.
Untitled1.jpg
how can i do that to bring my image 'i' like a normal CT image?
  1 Comment
Manjunath R V
Manjunath R V on 29 Apr 2021
Hello emerson can i get a code for hounsfield unit and to enhance the contrast of an ct image

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Answers (3)

KALYAN ACHARJYA
KALYAN ACHARJYA on 4 Sep 2019
Edited: KALYAN ACHARJYA on 4 Sep 2019
Read the individuals slices and convert them to binary, is there any issue?
slice_test=Y(:,:,400) % Just as example of slice number 400
bw_image=imbinarize(slice_test,method);
%...............................^ any specifice method,
% or delete method part, Matlab use for default Method
  2 Comments
KALYAN ACHARJYA
KALYAN ACHARJYA on 5 Sep 2019
Yes, the u result images are not binary image, do contrast streching (Gray Level Transformation), do check. I will reply in afternoon session

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Manjunath R V
Manjunath R V on 26 Mar 2021
even i want clarification like how to apply hounsifield unit to ct image ? for better details
  2 Comments
Manjunath R V
Manjunath R V on 25 Apr 2021
thank you for u r response will check the code that u have shared to me

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Manjunath R V
Manjunath R V on 25 Apr 2021
Edited: Manjunath R V on 25 Apr 2021
am working on liver segmentation on CT dataset i need a help regarding labeling of a image since am using sementic segmentation
imDir = fullfile(dataSetDir,'Inp_256'); this is my input original dataset or training data
input image attached here for ref
pxDir = fullfile(dataSetDir,'lab256'); this is my labeled data of the training data
labeled image for the input image attached here
this dataset i found in 3DIRCADB where it contains both training data as well as labeled images and masks for that training data
now my query is to train my network i should use oly training data as well as labelled data rite?
is labelled data whatever they have given is it enough to train my network

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