Hi Daniel,
I am using few toolboxes via SPM GUI. some, such as WFUPickAtlas , Marsbar, ArtRepair, are available in the GUI under "toolbox"
Other toolboxes are available in the GUI batch under the SPM>tools. All folders of these tools are in the SPM folder under "spm12/toolbox"/.
Here is a link to the installation of some tool and explanation for how to implement it in SPM: https://www.nitrc.org/projects/clinicaltbx/
I found information there for how to make it available in SPM GUI. Maybe you could find relevant information there or ask the developers directly.
hope this helps.
Tammar
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