Hey All!
I was wondering, I really don't like DTI studio all that much, and I was wondering what kind of tools you use to visualize fibers? Is there a way to visualize fibers in MIPAV?
I've been trying out different tools, such as MedINRIA, slicer3D and such, but cannot decide on the best of them.
Translation from the JIST-made fibers (in vtk file format) and those programs isn't all that clear. (Fibers are apparently not inside the brain, something with the volume origins me thinks.)
So, to prevent repeating work that others have already done, I would like have some discussion on what tools you guys/gals are using to manipulate your fibers once you've calculated them with your fine JIST pipeline.

any suggestions?

Daniel

Well, there hasn't been a reply to my previous question, so I'll try another, more limited one:
For those of you working with DTIstudio;

Have you managed to visualize/manipulate fibers you've created using the FACT module in JIST lately?

I cannot, so please humor me and track some fibers using the test data I attached here.

I can't figure out whether this is something new, or an older problem, or if I've just completely forgotten how to do this.

thanks,
Daniel

(My system: Windows XP, 3GB RAM, DTIstudio v3.0.2, JIST beta1.10)

Hi Daniel,

I may see what you mean - thanks for including your DTIStudio version info :)
Using a somewhat newer version of JIST, I can visualize ALL fibers in DTIStudio (see attached).
However, I can't seem to select fibers using their ROI tools (see attached "_oops").
Is this what you observe??

The newer DTIStudio releases must have changed how they deal with these ROIs - an older version
(2.4) works fine using these JIST fibers.

It may take some time to figure out how to make our fibers play nicely with newer DTIS...

Hey John,
Thanks for your time, I appreciate it.
At the moment, I cannot even reproduce your results, that is visualize 'all' fibers.
Reading in a fiber.dat file from JIST doesnt work properly. (See screenshot)
According to DTIstudio, all 28000 fibers run trough a single voxel!
What version of FiberTracker (FACT) are you using? My latest version is 1.4 RC.

Also, I am posting a bug report on the tracker, as this version fails in the process manager.

Interesting, thanks for the update and bug post. I'm also using FACT 1.4RC.
I'll explore this in addressing the bug you posted.

By the way, how do you discover that DTIStudio thinks:
"all ... fibers run through a single voxel" ??

Well, I think that's just rubbish based on an empty fiber-file.
The screenshot I attached shows the fiber statistics window in DTI studio. It states that the number of voxels the fibers run through is 1. And that the total number of fibers (28k) is both the maximum and minimum amount of fibers/voxel. Doesn't make sense, but that's what I noticed.