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TOPIC: Extraction of fiber's data .fib VS .vtk file

Extraction of fiber's data .fib VS .vtk file 8 years 11 months ago #241

  • zebulon
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Hi,

In the lastest version of medInria, fiber's data was extract in a .fib file, in this version of medInria how extract this data ? I can't read the .vtk file.
In fact i would have a file like the example.txt attached.

File Attachment:

File Name: example.txt
File Size: 82 KB



It's possible ?

Thanks !
Last Edit: 8 years 11 months ago by zebulon.
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Re: Extraction of fiber's data .fib VS .vtk file 8 years 11 months ago #243

  • ocommowick
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Hi,

I am not sure which version you are talking about but I guess this is medinria 1.x series. We have changed completely the format for storing fibers in medinria 2. It is still called a fib file (that you can export using the browser workspace in medinria, right click export on the item).

We did this to stick much more to usual formats people encounter (the format we now use is purely a vtk one). We instead prefer to display the main values that were in the fib file inside the fiber bundling toolbox, once you filtered and validated your fibers of interest. If there are any stats you would like to see in that toolbox that are not there already, don't hesitate to tell us.
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Re: Extraction of fiber's data .fib VS .vtk file 8 years 11 months ago #246

  • zebulon
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Hi,

Thanks for your answer,

In fact with the bundling box or with a ROI we can select fibers and extract stats like FA, ADC, lenght (mean,max...)to this fiber of interest, but i would also extract the total number of fibers and the histogramme distribution of the lenght of this fibers filtered (10mm long fibers represente 12% of the total fibers, 20mm long fibers represente 24% of the total fibers...) :)

Thanks !
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Re: Extraction of fiber's data .fib VS .vtk file 8 years 11 months ago #248

  • ocommowick
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These are interesting properties we have not available yet indeed. We have been thinking for quite a while about improving this stats part in the diffusion workspace. I cannot promise you we will be able to do it very soon, but we'll definitely keep that in mind for the next medinria minor release (2.2).

In the meantime, I'm afraid the only thing you could do is to export the overall fibers and switch to some home made vtk tools to filter them and compute those stats. VTK has got all you need for what you'd like to have but that will of course be much less user-friendly.

Thanks for your feedback
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Re: Extraction of fiber's data .fib VS .vtk file 8 years 11 months ago #258

  • zebulon
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Hi ocommowick,

Concerning your last post, if it will possible in the medInria minor release (2.2) to extract total number of fibers and the histogramme distribution of the lenght, do you know when this release will become available ?

Thanks a lot

Aurélien
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Re: Extraction of fiber's data .fib VS .vtk file 8 years 11 months ago #261

  • ocommowick
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Hi,

That is a very good question. We have great things in mind for this next release and as usual we'll need to choose some tradeoff between the release date and the features incorporated. We hope to have a fixed release schedule in the future (something like every 6 months between each minor release), but then I cannot guarantee yet that this feature will be included.

In any case, we'll keep you posted, either here or through the announce list to which you can subscribe if this is not done yet : med.inria.fr/contact
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