[Mrtrix-discussion] Default values for trials and initcutoff

[Jesse Ross-Jones]

Dear Mrtrix Devs,

I was trying to find the default value for* trials (set the maximum number
of sampling trials at each point (only used for probabilistic tracking). *)
and for *initcuttof*. I began with reading the code in streamtrack.cpp and
I see that there is a list of defaults

Tractography::Properties properties;
  properties["step_size"] = "0.2";
  properties["max_dist"] = "200";
  properties["min_dist"] = "10";
  properties["threshold"] = "0.1";
  properties["unidirectional"] = "0";
  properties["stop_when_included"] = "0";
  properties["no_mask_interp"] = "0";
  properties["sh_precomputed"] = "1";

Any values placed here will overwrite values from the previous section on
options and will be replaced if the user provides an alternate value.
However, when no value is given by the user and a default is not provided
in the above list, the default is taken therefore from the options section?:

Option ("cutoff", "cutoff threshold",
      "set the FA or FOD amplitude cutoff for terminating tracks (default
is 0.1).")
    .append (Argument ("value", "value",
          "the cutoff to use.").type_float (0, 1e6, 0.1)),

  Option ("initcutoff", "intial cutoff threshold",
      "set the minimum FA or FOD amplitude for initiating tracks "
      "(default is twice the normal cutoff).")
    .append (Argument ("value", "value",
          "the initial cutoff to use.").type_float (0, 1e6, 0.1)),

Option ("trials", "number of trials",
    "set the maximum number of sampling trials at each point "
    "(only used for probabilistic tracking).")
    .append (Argument ("number", "number", "the number of
trials.").type_integer(1, 10000, 50)),

If these values are overwritten however, I am wondering when does the
initcutoff value get set to twice the cutoff value? (The original default i
see is 0.1 which is the same value for cutoff) Does this occur in another
file? *-initcutoff *(set the minimum FA or FOD amplitude for initiating
tracks* (default is twice the normal cutoff))

*
So my questions are these:

   1. Is the default value for trials when none is given by the user 50?
   2. When does initcutoff get set to twice the normal cutoff?

Many thanks

Jesse
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