Adding variance to scil_visualize_fodf #671
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Thanks for doing this @karanphil.
I seem not to have access to the shared data, so I could not test it. I'd be willing to give it a try if you put the data available again.
Otherwise, I tested the mosaic overlap script with structural data only and the changes introduced in here do not seem to have undesired side-effects.
It should work now! |
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Works fine with python 3.10! |
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This is simply an attempt to merge an old branch of @CHrlS98 into the main script
scil_visualize_fodf.py. With my simulations, I have a lot of repetitions of the same fODF reconstruction so I compute the variance of it. This addition allows us to view the variance as another fODF behind the "real" one, with the color of your choice. Note that you need to input the mean + some factor of the variance to get the right visual effect.Here is some data to test it. Also, it would be useful if users of this script try a typical command to confirm that I didn't break anything. @CHrlS98 @jhlegarreta
https://usherbrooke-my.sharepoint.com/:f:/g/personal/karp2601_usherbrooke_ca/EuPAjEN6VHlNi4-MGW3rjwcBCLNpkCRNuMD1F_K3PRxH8w?e=wY35T7
With this data, try:
scil_visualize_fodf.py wm_fodf_mean.nii.gz --variance wm_fodf_var.nii.gz --axis_name coronal --sph_subdivide 2 --bg_color 1 1 1 --color_rgb 0 0.65 0.35 --var_color 0.6 0.6 0.6, this will show the fODFs with a grey outline representing the fODF + 2 * std.