Hi Jon,
at least for MRI modalities I am not aware of processing steps that use a temporary folder. Can you give an example? Most image manipulation functions write their results to the same folder where the original files are. A few others put their files into MATLABs current working directory. To make sure no output gets lost or mixed up, I usually change MATLABs current working directory to a place where I want to drop these files.
Best
Volkmar
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