It seems like you are calling sum on 2D arrays, so each output would be a row vector, which you can't store within Output(i). You could instead store the vectors in a cell array:
replication=10;
signal_resolution_merge=2;
Output = cell(replication,1);
for i= 1:replication
Output{i} = sum(reshape(Final_result.nRx_raw_matrix_wout_noise(:,:,(i)), ...
signal_resolution_merge, size(Final_result.nRx_avg,2)/signal_resolution_merge));
end
or, if you'd like, a matrix (Output(i,:) = sum(...)).
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