findpeaks() needs a vector, whereas you are passing it a scalar. It will not work properly. Also, if the number of peaks is different, then you will need to use a cell array to store all values. Normal arrays can only hold values when all the dimensions are of the same length. Try something like this
u_atl=squeeze(u(:,:,1,:));%size(40x144x720)
pval = cell(40, 144);
ploc = cell(40, 144);
peak_ebb = cell(40, 144);
ploc_ebb = cell(40, 144);
for i=1:40
for j=1:144
[pval{i,j},ploc{i,j}] = findpeaks(squeeze(u_atl(i,j,:)), 'minpeakdistance', 6);
[peak_ebb{i,j},ploc_ebb{i,j}] = findpeaks(-squeeze(u_atl(i,j,:)), 'minpeakdistance', 6);
end
end
