You aren't using the loop index for anything, so nothing changes.
You don't appear to be preallocating anything.
Your entire setup assumes that there is only one blob in each frame when there's no assurance that there is.
Start over.
% contains a 288x384x31 logical image
% with only one blob per slice
load FMask.mat
% modify the test image for the sake of demonstration
% now we can't presume that there is only one blob per slice
FCombinedmask = FCombinedmask | flipud(FCombinedmask);
% if you're not keeping track of what your variables mean
% then use variable names which actually mean something on their own
nframes = size(FCombinedmask,3);
% preallocate
All_centroids = cell(nframes,1);
% do the thing
for f = 1:nframes
% actually use the loop index somewhere for something
% don't presume the number of blobs if you have no means to ensure that
S = regionprops(FCombinedmask(:,:,f),'Centroid'); % get the struct
All_centroids{f} = vertcat(S.Centroid); % extract each list of centroids
end
% number of centroids differ
celldisp(All_centroids)
