@stevenagl12 a couple of questions:
We are adding file export directly from the subject hierarchy tree (for example in Data module). The first iteration will probably only export a single file at a time, but soon we will add multiple item (and/or entire folder) export, which will write content of all the selected markup nodes into a single json file. From that file you can use a few lines of Python code, R code, or the Excel GUI to create a spreadsheet. Would that fulfill your needs?
We also have standard csv export in Markups module (Export/import table), which creates tsv/csv files like this:
We could easily implement multiple node export. Could this be improved/customized to fit your needs?
I agree that supporting multiple file formats for data storage is a huge liability and we ideally we would use a single format. However, supporting multiple file formats for data export would be probably fine, it should be just clear for the users that it is not for data storage, only for interoperability. These export options would not need to be added to the “Save data” window, they could be in separate module(s) or subject hierarchy right-click menu actions.
Among all discussed options however, this one sounds by far the most promising to me:
You can explore the available linear model tools in Python, and use them within Slicer/SlicerMorph. We can possibly work with you, if you want to go down that route
MorphoJ looks like a closed-source project, with no development community around it, based on 15-20 year old technologies and with a look and feel of about the same era. It still has about 500 mentions on Google Scholar per year, so there are users. This indicates that there is a huge opportunity here for an alternative software, which is similarly easy to use, but based on current technology, and it is open and reproducible. Maybe SlicerMorph could fulfill this need.
Probably all the algorithms that MorphoJ offers are available in various Python packages and Slicer/SlicerMorph has all the GUI components you may need, so what is missing is really just putting together convenient modules for specific analysis tasks that you are interested in. @muratmaga even offered to help you with this, so you would probably not need to invest a lot effort. Would you consider this option?