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It is technically possible to change the code to read subset of channels. It would not reduce heap usage because data is organized in blocks in which all data has to be read (then discarded).
Such change would require to change a collection of functions because all MFF files are interdependent - and likely generate more problems that it would solve.
Does the plugin feature restricted reading at all (either channel- or trial-wise)?
Or is this a limitation of the JAVA plugin? Such a feature might also reduce the large amount of heap required.
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