How to convert nii format file into 2D image - matlab

Question

I have a file with .nii extension. I don't know how to convert a .nii file into 2D format.My question is while converting .nii file into 2D, am I losing some information about the file.Which format is good? dicom or png or bmp.
nii = load_nii('im.nii');
size(nii.img);
returns
ans =
39 305 305
and it is in uint8 format
May I use squeeze or resize?How to apply resize to this image;whether it lose information?

Answer 1

Yes you can manipulate the image/sequence as you would with any array.
Here is a simple example with data available from the NIH here.
The data set is in 4D and is named "filtered_func_data.nii".
Let's load the dataset and access the img field of the resulting structure:
S = load_nii('filtered_func_data.nii')
Here, S is a structure with the following fields:
S =
hdr: [1x1 struct]
filetype: 2
fileprefix: 'filtered_func_data'
machine: 'ieee-be'
img: [4-D int16]
original: [1x1 struct]
And we can access the image data with the field img (you already figured that out):
A = S.img
If we check the size, we get:
size(A)
ans =
64 64 21 180
So the dataset consists in 64x64 images with a depth/number of slices of 21 and a number of frames of 180.
At this point we can manipulate A as we like to reshape, resize or anything.
Here is a simple code (animated gif) to loop through each slice of the 1st timepoint in the 4D array:
NumSlices = size(A,3)
figure(1)
filename = 'MRI_GIF.gif';
for k = 1:NumSlices
imshow(A(:,:,k,1),[])
drawnow
frame = getframe(1);
im = frame2im(frame);
[imind,cm] = rgb2ind(im,256);
if k == 1;
imwrite(imind,cm,filename,'gif', 'Loopcount',inf);
else
imwrite(imind,cm,filename,'gif','WriteMode','append');
end
pause(.1)
end
Output:
Which looks pretty nice to me.
So in your case, you get a size of [39 305 305] and you can apply the same manipulations I did to play around with your data set, which is in 3D.
EDIT
With your data it's the same:
S = load_nii('Subject01.nii');
A = S.img;
NumSlices = size(A,3);
And then, if you want a 2D image you need to select a slice in the 3D array.
For example, the first slice is accessed like so:
A(:,:,1)
And so on for the rest.
To save images as png, use imwrite.
Hope that helps!