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Hello
I want to add artifacts such as ”Spikes“, "N/2 Ghosts", "motion Artifacts", etc. to the original dwi (nii.gz format) images respectively.

Because there are hundreds of DWI data in total, it is too laborious to load and set parameters one by one in MITK's GUI interface and save them manually.

How to set various artifacts and corresponding parameters through the command line, process raw DWI data in batches, and save them in nii.gz format in different folders named after the artifact names?

Hope to get your help, thank you.

Hello, when I use MITK software, I want to save an image through Screenshot Maker, but there is a watermark on the image, how can I remove this watermark, thank you.

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).

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!

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 🙂

Hi Peter

I guess I do something terribly wrong when installing MITK

I downloaded MITK-v2021.02-linux-x86_64.tar.gz.
Unpacked it, added the main and bin subdirectory to my $PATH in my .bashrc and successfully started the Workbench
I can load nifty files, but when trying to a load a .trk tract file generated with TractSeg (trk_legacy format) I get the error
"no reader available..."

Any, idea what I might have missed?

Many thanks in advance
William

The links to download MITK Diffusion point to files from this folder https://www.mitk.org/download/diffusion/nightly/

Looking at the links, I noticed that Ubuntu has two versions of the MITK plugin : 2020 and 2022. However, only the 2020 version is available for Windows.

Considering that the latest release v1.2.0 is dated 2020, I suppose the 2022 version is either a "nightly" or a patch. Am I correct? I am actually asking if the 2022 version contains meaningful changes compared to the 2020 version.

Hi,

i have the following files:

1. CST L on t1.nii.gz. Corticospinal fiber tract overlaid on a t1 image and saved as nifti.
2. CST L.zip. Corticospinal fiber tract saved as trk (inside the zip file).

I can display them correctly on trackvis and freeview (from freesurfer). But when i try to view them in Mitk Diffusion they are not correctly overlaid.

As far as i can tell the trk file is correctly populated and since i can view them on the other 2 applications i think that Mitk Diffusion has a bug.

Any thoughts?

Thanks

Hi, I am trying to use MITKFiberDirectionExtraction to transform my own tck file into TOM, which is used for TractSeg model. However, I was stuck on how to install this software for Windows 10 and run the function. Could you please teach me how to install this, or can I show my own data for help? Thanks for your help!

When I start MITK, I get the following error：
core.mod.python.svc: Initializing python service
Fatal Python error: initfsencoding: unable to load the file system codec
ModuleNotFoundError: No module named 'encodings'
I am sure my python contains the 'encodings' module and I have installed all packages in PythonRequirements.txt, python version 3.11.4. I have no problem using the non-Python version, is there any way to solve it? Or will the python version of dMRI simulation be faster

The MITK Diffusion plugin's documentation is missing on docs.mitk.org.

A linkless org_mitk_gui_qt_diffusionimaging list item is present in the List of Plugins for End User Use on the MITK Plugin Manuals web page for diffusion imaging. I tried to enter the following URL manually in my web browser, but in vain : https://docs.mitk.org/diffusion/nightly/org_mitk_gui_qt_diffusionimaging.html.

Also, there is no entry for diffusion imaging on the API Reference for MITK Plugins page. Is this normal?

However, by searching in the search box on the docs.mitk.org/diffusion website, I was able to find the page private plugins Directory Reference in which the API Reference for org.mitk.gui.qt.diffusionimaging is located. Is it normal that this is private and difficult to find?

Hello
In the user manual it says there is a python plugin but I can't find it anywhere. The manual also uses an image of an old version, in the new version there is no button with the python logo.

version: MITK Workbench v2022.04

Is there also a reason version 2016 has more segmentation methods than 2022?

thanks

Hi everyone,

i am currently trying to simulate diffusion data for an experiment using Fiberfox. After inputting a tractogram and setting the simulation parameters, i am able to obtain my diffusion data. However, when running my analysis, I realised that some of the FODs are perpendicular to the input fibers? This effect is also present when looking at the raw diffusion glyphs. I am unsure what the problem is, as I've tested different simulation settings and tractograms. Bvals and bvecs are set to the HCP protocol.

Hopefully it is just a problem with my settings, but would be grateful for insights whats going wrong here !

Cheers
Philip