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MIC-DKFZ / MITK-Diffusion

MITK Diffusion - Official part of the Medical Imaging Interaction Toolkit
http://mitk.org/wiki/MITK
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[Fiberfox] Save & Load Parameters Missing For Fiber Generator #6

Closed benoit-dubreuil closed 4 months ago

benoit-dubreuil commented 2 years ago

The following Save Parameters and Load Parameters buttons do not save and load parameters for the Fiber Generator tab; they save and load parameters for the simulation tab (Fiberfox).

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Also, the Fiber Generator parameters aren't saved in the Fiberfox parameter file (.ffp) file either.

I'm looking for a way to save and load parameters for the Fiber Generator in order to automate that process. Naturally, being able to call MitkFiberfox.(bat | sh) for only generating fibre bundles is expected. The goal is to feed the resulting fibre bundles to other algorithms that need testing.

EDIT

By looking at the source code, I found this .cpp file : https://phabricator.mitk.org/source/mitk-diffusion/browse/master/Modules/DiffusionCmdApps/Fiberfox/Fiberfox.cpp. So then I thought Maybe there is a command-line tool for generating fibre bundles that I haven't found yet?. Well, I did find the MitkRandomFiberPhantom.(bat | sh) command-line tool. Good!

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However, by reading the command-line options for the tool, I noticed that the parameters are low level. What I mean is that, in order to generate certain fibre bundle configurations (or "shapes" as called in the research article Fiberfox: Facilitating the Creation of Realistic White Matter Software Phantoms), one needs to configure many parameters to describe the shape they are trying to generate. Supporting high level parameters separated into categories for each fibre bundle shape would increase the simplicity of use of the toolset.

Is there documentation or examples (examples are really useful) for the command-line tool MitkRandomFiberPhantom.(bat | sh)?

EDIT 2

After speaking to my peers and professors, and reflecting on the situation, we realized that we should try other simpler tools than MITK Diffusion / Fiberfox for generating white matter fibre bundles.

Thank you for your help, it was greatly appreciated @peterneher 🙂

peterneher commented 2 years ago

Hi Benoit. Just for the sake of thread-completeness: the fiber generation parameters are also saved. They are in the same file as the simulation parameters. Nevertheless, I never implemented a command line tool for the "manual" fiber generation, only for the random fiber generation, which is the MitkRandomFiberPhantom tool that you found. The fiducial-based fiber generation is only possible in the GUI.

benoit-dubreuil commented 2 years ago

Just for the sake of thread-completeness: the fiber generation parameters are also saved. They are in the same file as the simulation parameters

Well then, there's is probably a bug because I tested this before, but in vain. On my end, random fibre generation parameters are unfortunately not saved.

peterneher commented 4 months ago

Two years late, but yes. This is apparently not implemented.