Dear Eloy,
if you want to implement a new tool that uses SPM functions it might be easiest to create an SPM toolbox and a batch configuration file that integrates your tool into the batch system. This tool could then be run from the batch system itself (via scripts or GUI) - there is no need to get the data out of the batch system before you can run your tool. Feel free to contact me off-list if you need any guidance for that.
If your tool is more interactive, you might want to look at spm_input or spm_getfile instead.
Best,
Volkmar
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