How to display images from nifti file format in Matlab?

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Matthew Worker
Matthew Worker 2020-5-20
编辑： John Kelly 2023-12-7
I have a COVID-19 CT segmentation dataset where all images are in .nii file format. Each image file has mulitple slices (512*512*100). Using niftiread command Matlab i read the image file and now I want to visualizing each of the 100 slices one by one in Matlab.
The dataset is available on the site http://medicalsegmentation.com/covid19/
  1 个评论
Tanguy
Tanguy 2020-9-14
编辑：John Kelly 2023-12-7
imtool3D_td would perfectly fit your needs, and also display Mask with edit tools (ex: brush tool).
Simply run the following command after adding imtool3D_td to your Matlab path:
V = niftiread('niftifile.nii')
Mask = niftiread('mask.nii')
tool = imtool3D(V);
tool.setMask(Mask);
Use scrollwheel to go through slices.
You should get this :
Other examples on the github page or the help function of imtool3D.m Good luck
Hope that helps!

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回答（1 个）

Emerson Nithiyaraj
Emerson Nithiyaraj 2020-5-20
After you read the Nifti file using niftiread, you could visualize each slice one by one using the below command,
V = niftiread('niftifile.nii');
c = V(:,:,n); %n is the slice number that you want to visualize.
imshow(c,[])
Or else there is an online tool ,Papaya: a pure JavaScript medical research image viewer, supporting DICOM and NIFTI formats, compatible across a range of web browsers. So this is like an radiologist assist tool where you could have a better understanding about the nifti file here rather than reading slices one by one using Matlab.
Link: http://ric.uthscsa.edu/mango/papaya/index.html
  2 个评论
Diannira Sasri Apsari
Diannira Sasri Apsari 2020-9-3
I need to display .nii file on specific slice but the output is blank. How to solve it?
This is my code
for j=3
V = niftiread('label0001.nii');
info = niftiinfo('label0001.nii');
refImage = V(:,:,j);
imshow(refImage,[])
title('Ground Truth Image');
end
Emerson Nithiyaraj
Emerson Nithiyaraj 2020-9-4
You have used 'j' as the slice number. So 'j' denotes the particular slice number that you want to display. For example if you want to display the 100th slice;
Try this code
V = niftiread('label0001.nii');
info = niftiinfo('label0001.nii');
j = 100;
refImage = V(:,:,j);
imshow(refImage,[])
If you want to display groundtruth try,
V = niftiread('label0001.nii');
info = niftiinfo('label0001.nii');
j = 100;
refImage = V(:,:,j);
imshow(refImage)
Still if you have problem, convert the data format of the particular slice to int16 or int8.
Please let me know the feedback.

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