I'm calling the command-line version of MCFLIRT from within another C program, using system(). My
results have been good. However, it takes a very long time to read in the image data file (about 185
MB per data set), and another very long time to write out the image data file. Then, because MCFLIRT
writes out .nii.gz file, I have to spend even more time gunzipping the output.
I'd like to speed up this process in any way I can. For example, would it be possible for me to supply
my image data to mcflirt via a pipe to standard input, and/or to receive the output via a pipe to
standard output? Failing that, is there some way for me to ask mcflirt not to gzip the output, so that
I wouldn't have to spend time gunzipping it?
Thanks in advance.
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