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frankyeh / DSI-Studio

A Tractography Tool for Diffusion MRI
http://dsi-studio.labsolver.org
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Not sure which threshold is used and if its value is randomly chosen or not #55

Closed JohannesWiesner closed 3 years ago

JohannesWiesner commented 3 years ago

I am using dsi_studio --action=trk without any input for fa_treshold. According to the docs this means that

If fa_threshold is not assigned, then the default Otsu's threshold will be used

which (again according to the docs) should equal 0.6 by default. However, when I load my .fib file into DSI Studio and add the resulting .tt to it, I get the following information about the .tt file in the lower right corner of the UI:

A deterministic fiber tracking algorithm (Yeh et al., PLoS ONE 8(11): e80713, 2013) was used. A seeding region was placed at whole brain. The anisotropy threshold was randomly selected. The angular threshold was 55 degrees. The step size was 1 mm. Tracks with length shorter than 10 or longer than 400 mm were discarded. A total of 100000 tracts were calculated. parameter_id=c9A99193FE8D5123Fb803Fcb2041bC843A08601ca01cbaCDCC4C3Ec

Is this just misleading information derived from the .tt file or did DSI Studio really chose the threshold randomly during fiber tracking? If I don't specify fa_threshold, then otsu_treshold with a value of 0.6 should be chosen? Why does "The anisotropy threshold was randomly selected" sentence then appear in the UI?

frankyeh commented 3 years ago

Sorry for my inaccurate description (I am correcting them now).

If fa_threshold is not assigned, DSI Studio will use 0, which selects a value between [0.5 Otsu, 0.7 Otsu] using a uniform distribution.

Best regards, Frank

On Tue, Jun 1, 2021 at 11:35 AM JohannesWiesner @.***> wrote:

I am using dsi_studio --action=trk without any input for fa_treshold. According to the docs http://dsi-studio.labsolver.org/Manual/command-line-for-dsi-studio this means that

If fa_threshold is not assigned, then the default Otsu's threshold will be used

which (again according to the docs) should equal 0.6 by default. However, when I load my .fib file into DSI Studio and add the resulting .tt to it, I get the following information about the .tt file in the lower right corner of the UI:

A deterministic fiber tracking algorithm (Yeh et al., PLoS ONE 8(11): e80713, 2013) was used. A seeding region was placed at whole brain. The anisotropy threshold was randomly selected. The angular threshold was 55 degrees. The step size was 1 mm. Tracks with length shorter than 10 or longer than 400 mm were discarded. A total of 100000 tracts were calculated. parameter_id=c9A99193FE8D5123Fb803Fcb2041bC843A08601ca01cbaCDCC4C3Ec

Is this just misleading information derived from the .tt file or did DSI Studio really chose the threshold randomly during fiber tracking? If I don't specify fa_threshold, then otsu_treshold with a value of 0.6 should be chosen? Why does "The anisotropy threshold was randomly selected" sentence then appear in the UI?

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JohannesWiesner commented 3 years ago

Hi Frank, thanks so much, now it's more clear what DSI Studio is doing behind the scenes :) Feel free to close this issue!