Argument skip_b0_check always overwrites with minimum

[karanphil]

I think there might be a major bug with how we deal with the b0 checks. A bit of context:

• The argument b0_threshold sets a maximum value for the b0s.
• The fonction check_b0_threshold in scilpy.gradients.bvec_bval_tools then compares the b0_threshold with the minimal b-value min_bval.
• By default, if the min_bval is higher than b0_threshold, it will raise an Error.
• The skip_b0_check allows us to raise a warning instead and overwrite b0_threshold to be the same as min_bval.
• However, there is no way to raise the warning but keep the b0_threshold as is.
• The add_skip_b0_check_arg function has a will_overwrite_with_min argument that seems completely useless and even misleading, because it only affects the help message but not the behavior of skip_b0_check. For instance, I tought that will_overwrite_with_min=False would keep the b0_threshold as is. This is important in cases where you have no b0s and don't want to take the lowest shell as a b0.

My question is: What is the use of this will_overwrite_with_min argument, which is even mandatory. Am I missing something?

I think we should find a way to pass the bool value of will_overwrite_with_min to the check_b0_threshold function, or split the function in two (skip_b0_check and overwrite_b0_thr_with_min).

[karanphil]

I will do some tests to understand better the edge cases.

[EmmaRenauld]

I thought we did that together and with Max but maybe in the end we forgot to change something. I will try to check again too.