How to read data file in batch until end of file and write results in an array

I need to read a large bin file in batches. Assuming the batch size is 5000 and will take an average over K (100 in this case) bin. At the end of process, I will have a number of averages to plot.

Have the basic code (first 5000 batch) below and now I have a couple of questions to proceed:

%%Process and Plot rf.bin 
filename='rf.bin';                                     % filename='./rf.bin';
fid=fopen(filename,'r');
dataHeader=fread(fid,123,'uint8');                     %skipping the header for .bin
NsperBatch = 0.5e4;                                    % number of sample per batch 
magSpectrum=0;
for k=1:100                                            % There are roughly 13243 sets
    data=fread(fid,NsperBatch*2,'int16','b');          %16 bit integer big endian
    dataIQ=data(1:2:end)+1i*data(2:2:end);             %convert to complex IQ
    dataSpectrum=fftshift(fft(dataIQ));                %convert to frequency domain
    magSpectrum = magSpectrum + abs(dataSpectrum).^2;
end
magSpectrum = magSpectrum/100;
z=pow2db(magSpectrum);                                 %convert magnitude to DB   
fclose all;

1. How do I continue to read until end of file. Roughly, there are about 13243 sets/batches until end of file

2. How do I store all end results in an array (like Z=[5000, 13243]), so they can support the 3D plot later.

thanks!