Diffusion and Tractography on rats

[Maurizio Bergamino]

Hello,

I am working on DTI and tractography on rats. I have never worked with animals, and I am not sure if my b-vectors are correctly oriented.

This is because, if I use DSI Studio and bruker2nifti (python), I have two different b-vectors files.

I tried to double-check the orientations by using FA and V1, but I am not sure...

Is there somenone here that can help me?

I could share the data.

Thanks,

Maurizio

[Eleftherios Garyfallidis]

Hello Maurizio,

I know in human data, people use the average length of the relatively long streamlines as a cost function for correcting 

any b-vector orientation issues. So the largest average should give you the correct orientation. 

I am not sure if this idea works well with other animal brains too. But worth a try?

Any other suggestions? Kurt?

Best,

Eleftherios

--
You received this message because you are subscribed to the Google Groups "Diffusion-imaging" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diffusion-imag...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/diffusion-imaging/59b1e84e-8491-4d9d-a7f5-a51e46892bcen%40googlegroups.com.

[Maurizio Bergamino]

Hi,

thank you for the good suggestions.

I tried to use together FA and V1. The orientations look correct, but I am not sure about some areas. Also, because I do not know well the rats' anatomy like the human one.

I will try the python code to test flips / permutations.

Thanks also for the paper.

Maurizio

On Tue, Apr 20, 2021 at 11:25 AM Schilling, Kurt G <kurt.g.sc...@vumc.org> wrote:

Hi Maurizio,

 

Yes – there are some good tests you can do.

 

Unfortunately, looking at FA alone will not tell you anything about orientation. A visual check of the primary eigenvectors can usually give insight into different flips/permutations of the b-table.

 

We have also worked on a python code to test flips/permutations: https://github.com/scilus/scilpy/blob/master/scripts/scil_validate_and_correct_bvecs.py

From our article in 2019 in MRI. This is actually implemented in DSI Studio too as “check b-table” option.

 

If you want even slightly higher angular precision (more than just flips and permutations), Ben Jeurrisen validated the algorithm Eleftherios mentioned (https://pubmed.ncbi.nlm.nih.gov/24968247/). I believe this is implemented in MRTrix, however, I have not used it.

All of these “should” work in animal models, however, we did validate in human so I’m not positive!

 

Let me know if you have any issues implementing these, or if results do not seem as expected.

 

Thank you,
Kurt

[ WARNING : This email came from an external source. Please treat this message with additional caution.]

[Do Tromp]

Hi Maurizio!

Generally I use Camino's pdview to visually inspect the tensor directions. See my post on this topic here: http://www.diffusion-imaging.com/2014/03/dti-quality-control-part-2-tensor.html

Even in rodents the corpus callosum provides a great landmark to visually check if the tensors are pointing in the right direction. 

Let us know what your experience is with the python code. I've been looking for an automated way to check if the b-vectors were applied correctly.

All my best,

~Do

To view this discussion on the web visit https://groups.google.com/d/msgid/diffusion-imaging/CAPoSmHHXuh7R5vYMEW-WasWha-ii8HRE6mEn6%2BeY55diQmK%2BqQ%40mail.gmail.com.

-- 

Do Tromp, PhD

www.dotromp.com

Owner Davis Coworking

www.davis-coworking.com

[Maurizio Bergamino]

Hi Do,

thanks for your help.

I will try to work on a Python code for that. I will let you know.