How can I loop fread through the same data file multiple times ?

I have a large binary related to 1 hour recording from 16 electrodes (each of them part of a "pair"). The binary data has in the file the following structure: 1 = time 2 = channel 1 3 = channel 2 ... 17 = channel 16

I am trying to loop fread in order to load a segment of 1 minute for each channel, perform some analysis, save a mat file and repeat with the following channel. The script works for a single channel using a while loop. I am trying to put the while loop nested in a for loop by setting the parameter "activepair" as variable from 1 to "total number of pairs in my data"

activepair=1; %this value is set at the beginning to select the pair. Here is where I want to put a "for" cycle to go from 1 to N pairs, depending on what's in the long binary file.

while ~feof(FID)
    tic
    index=index+1;          % second number
    currData=fread(FID,[Fs*60*(n_channels+1),1],'double');  % read one minute of data in 2D array
    disp(sprintf('Processing minute: %d',index))
    disp(sprintf('Processing pair: %d',activepair))  

      %%loading channel 1
      time = currData((1:(n_channels+1):end), 1);
      data1= currData(((activepair+1):(n_channels+1):end), 1);
      trace1 = [time data1];
      seg1 = transpose(trace1(:, 2));
     %%load channel 2
      data2 = currData(((activepair+2):(n_channels+1):end), 1);
      trace2 = [time data2];
      seg2 = transpose(trace2(:,2));

...CALCULATIONS HERE...  

      toc
      if index > 59, break, end ;  %this line prevents the cycle to attempt analyzing data starting at the end of the last segment, as a while cycle would normally try to do. In case of recordings shorter or longer than 60 minutes, modify the value as "end-1" minutes (z.b. 29 for a 30 min recording)
  end

However for some reason the script is not able to repeat. the variable currData results empty at the end of the first while loop and I receive an error related to the inconsistency of the matrix sizes used... I think somehow the reference to the beginning of the file... where fread should start, gets lost somewhere but I am not sure this is the issue.

[dpb]

Well, by the end of the while loop you're at EOF so any further fread after that is bound to return empty.

I don't see any frewind or fseek to set the file pointer back to the beginning or the location of a timestep data segment anywhere.

You might want to look at memmapfile as way to build structure of the internal storage that can then address at higher level.