Antoine,

One workflow that works fast for me, for large data files, is to load first the 
whole file with mgetl, then remove all empty lines using isempty in a loop (as 
shown below), process the header block, isolate the data block and save it to a 
temporary backup file to disk using mputl, then load very efficiently from disk 
that backup file using fscanfMat.

tlines= mgetl(fid,-1);  // reads lines until end of file into 1 column text 
vector
bool= ~cellfun(isempty,tlines);
tlines= tlines(bool);    // removes empty lines

function out_text=cellfun(fun, in_text)
// Applies function to input text (column strings vector), line by line
  n=size(in_text,1);
  for i=1:n;
     out_text(i)=fun(in_text(i));
  end
endfunction


Regards,
Rafael
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