How to display images from nifti file format in Matlab?

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/

[Tanguy]

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!

Answer 1

[Emerson Nithiyaraj]

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

[Diannira Sasri Apsari]

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]

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.