Dear FSL experts and users,
For a while now I have been using FSL’s Diffusion Toolbox (FDT) and I have some questions regarding the outputs I am getting from doing probabilistic tractography.
After running the preprocessing pipeline and bedpostx, I run probtrackx with multiple masks. To be specific, my seeds are 2 spherical ROIs (radius=15mm). The spheres are in standard space so when I run probtrackx I also include a standard-space-to-native-space matrix and the resulting connectivity distribution I get for each subject is in standard space as well.
When I run probtrackx I use all the default parameters (eg. Number of samples=5000, curvature threshold=0.2, max number of steps=2000, step length=0.5mm etc)
Here is my question: When I visualize each subject’s probability distribution (fdt_paths) on fslview, the intensity (brightness) values on the top toolbar are not 0-5000 but 0-a random number which is different for each subject. My understanding was that what should be displayed there is the max number of samples that went through each voxel.
I read online though that that the max number is 5000x(the volume of the ROI). The problem is that this multiplication does not make sense in my results.
Here is an example:
Subject x: intensity range (0-27953) 15mm ROIs: fslstats sphere1 –V = 1791 14328.0000
Subject y: intensity range (0-26961) 15mm ROIs: fslstats sphere1 –V = 1791 14328.0000
And here is an example with r=6mm ROIs and the same probabilistic tractography method:
Subject z: intensity range (0-225) 6mm ROIs: fslstats sphere1 –V = 123 984.0000
I would be grateful if someone could explain to me the numbers I am getting. How are the “27953”, “26961”, and “225” calculated?
Thank you!
Sincerely,
Nasia Metoki
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