How to visualize every frame of an fmri image

I have an fmri image and I'm opening it udìsing load_nii and the implay. Now I would make a for cycle to select rois for every frame, but I don't know how to do it, some of you know it?

I did this code but I don't know how I could go on:

nii = load_nii(filename);
data = im2double(nii.img);
implay(data);

Thanks, Carlotta.

Answer 1

[Prashant Arora]

I am assuming that "nii.img" returns a 4-D matrix of true color images and you would like to select ROIs for each frame using a loop. You can use the following code to create a interactive "ROI" polygon selector. The final "ROIs" will be stored in the mask variable as logical 3-D array.

nii = load_nii(filename);
I = im2double(nii.img);
mask = zeros(size(I,1),size(I,2),size(I,4));
mask = logical(mask);
for i = 1:size(I,4)
    figure(1)
    imshow(I(:,:,:,i))
    BW = roipoly;
    mask(:,:,i) = BW;
    figure(2)
    imshow(mask(:,:,i));
end

Answer 2

[Carlotta Fabris]

Thank you for the answer, but I don't have to draw new ROI. I have to consider the information of the clusters and masks I already created. For example if I'may considering the auditory network, I load the file .nii.gz that I did with FSL and I have to see which value has the cluster in a specific area. When I have that number, I have to take all the vowels that belong to that cluster and for each voxel I have to extract the time course. Then I should do the mean of all the time courses of an area.

This is the pseudocode I did:

nii = load_nii('Auditory.nii.gz');
data = im2double(nii.img);
implay(data);

for i = 1:size[data]
    voxel_value = data[cluster];
    for voxel_value = 1:size[voxel_value]
        M = voxel_value;
        for M = 1:size[M]
            N = extract_timecourse(M);
            Time = matrix[MxN];
        end
        mean(Time);
    end
end

Maybe now it's clear. Thank you again, Carlotta.