Hello everyone,
I am puzzled with something. I have been using Diffusion Toolkit and TrackVis to perform deterministic tractography and I have been extracting uncinate fasciculi.
I obtain the mean FA, MD, RD, and AD values automatically from TrackVis just by loading the respective maps to the software. Here is what's interesting: If I save the uncinate fasciculus I created as a NIFTI file (.nii) and then try to get the mean FA, MD, RD, and AD values from that NIFTI file using fslstats, the mean values I get are completely different from the values TrackVis gives me.
This is the syntax I use : fslstats -k -M
Why is this happening? Shouldn't the mean values be exactly the same? In some cases I am getting mean values from FSL that are smaller than the minimum FA values of TrackVis so we are talking about very diverging values.
Thank you!
Hi Haykel,
Thanks for your answer. This was not exactly what I was asking, let me rephrase.
I have done preprocessing using FSL. Then I used Diffusion Toolkit to perform data reconstruction and fiber tracking on my diffusion images. Afterwards, I ran TrackVis to visualize the fibers of tractography and extract uncinate fasciculi.
When I create, say, the right uncinate for subject A, TrackVis gives me a mean FA value for this whole right uncinate. If I choose to save this uncinate as a NIFTI file though, and try to obtain the mean FA using the FSL command I mention in my initial question, then I get a mean FA values that does not match the mean FA values TrackVis gives me.
So I wonder how this is possible. Both images (.scene from TrackVis and .nii) are images of the same uncinate. How is it possible that the two softwares give out different mean FA values?
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