From FSL to Trackvis

[sandrokhan80]

Dear Do,

You cannot even guess how much I like reading your blog! A gold-minner of interesting infos and ideas for who is still a newbe in diffusion imaging.
Maybe it's a very banal question but .... producing appealing images is the funniest part of neuroimaging after all!
My lab is all based on FSL (and Freesurfer) and I'm really unsatisfied of visualizing my results only in RGB maps on fslview. I'd love using a powerful visualization tool as Trackvis but it seems that scalar maps produced on FSL are not compatible with the Trackvis format. I know there is a Camino-to-Trackvis tool and I was wondering if it exists a similar software or another reasonable way for using FSL scalars on Trackvis. Another question is if Trackvis is limited to deterministic tractrography or I can consider to use it also for data from probabilistic tractrografy.

Thanks for your help

Alessandro

[Do Tromp]

Hi Alessandro!

That is great to hear, and I agree that making beautiful images is very rewarding indeed!

I do not have a lot of experience with the DTI tools of FSL (incompatibility with TrackVis being one of the reasons), but what I gather from the TrackVis help forum is that FSL and TrackVis are indeed not very compatible (http://trackvis.org/blog/forum/trackvis-usage/nifti-to-trackvis-format/). 

Your question did make me search around a little and write this post:

www.diffusion-imaging.com/2013/09/dti-tutorial-for-fsl.html

And it seems like MedINRIA is compatible with FSL. You can find their software here: med.inria.fr

Let me know how it goes!

Probabilistic tractography is usually saved in a different format that is not exactly 3D compatible. You could still visualize it like deterministic tractography but it would need a little more hands-on tweaking/programming . 

Hope this helps!

~Do

[sandrokhan80]

Il giorno martedì 22 ottobre 2013 00:34:04 UTC+2, sandrokhan80 ha scritto:

Dear Do,

thanks for your advice, I tried MedInria and I found the software is rather compatible with FSL and Camino beeing all based on NIFTI format. Unfortunately In my personal opinion MedInria is a DTI tool not so complete and rich of option as FSL or Camino and in visualization it is not at same level of Trackvis. In any case I'm happy to have learned more about this software. MedInria forces me to start from the beginning and re-calculate scalar maps and tensor, It's impossible using the scalars and tensor I have already created with FSL. In any case MedInria create good deterministic tractography and it is also good in visualization. The only problem I found is a difficult use of ROIs for the selection of the tract of my interest. In MedInria it seems also impossible visualising probabilistic tractography.
Recently I discovered Fiber Navigator and it seems able to satisfy my needs,
1) I can use the scalars and tensor I already created with FSL or Camino;
2) It's great in visualization of deterministic tractography;
3) It's the only softare I found able to visualizing the probabilistic tractography I created in FSL.
The only real problem of the software is the total lack of a manual that is very disappointing.

Thanks for your kind reply and for the post in the blog. Excuse me for the delay in my reply (very busy with clinical stuffs in this period).
Love your blog ;-)

greetings from Italy,

Ciao

Alessandro