Options
=======

To display the options of Mouseflow, please use
``nextflow run scilus/nf-mouse_flow -r 0.1.0dev --help``.


Options list
------------

``--b0_thr_extract_b0 MAX_VALUE``  (default: 100)
    All b-values below a maximum value are considered b=0 images.

``--dwi_shell_tolerance TOLERANCE`` (default: 20)
    All b-values to +-tolerance are considered as the same b-value.

``--laplacian_value VALUE`` (default: "0.1mm")
    Fractional Intensity threshold (-f for the bet FSL command) for preliminary DWI brain extraction.
    See FSL bet documentation for more info.

``--run_eddy BOOL`` (default: true)
    Run Eddy.

``--run_N4 BOOL`` (default: true)
    Run N4 correction.

``--n4_convergence VALUE`` (default: 150x150x150x150)
    Number of iterations.

``--n4_threshold VALUE`` (default: 0.001)
    Convergence parameter which can halt execution of each level.

``--fodf_at VALUE`` (default: 0)
    Absolute threshold on fODF amplitude.

``--fodf_rt VALUE`` (default: 0)
    Relative threshold on fODF amplitude in percentage.


Optional Local Tracking arguments
------------

``--run_local_tracking BOOL`` (default: true).
    [LOCAL] Run Local Tracking.

``--local_seeding_mask_type TYPE`` (default: wm)
    [LOCAL] Seeding mask type [wm, interface, fa].

``--local_fa_seeding_mask_threshold THRESHOLD`` (default: 0.1)
    [LOCAL] FA threshold for FA seeding mask.

``--local_algo ALGO`` (default: prob)
    [LOCAL] Tracking algorithm [prob, det].

``--local_seeding SEEDING`` (default: npv)
    [LOCAL] Seeding type [npv, nt].

``--local_nbr_seeds NBRSEEDS``  (default: 10)
    [LOCAL] Number of seeds related to the seeding type param.

``--local_step SIZE`` (default: 0.05)
    [LOCAL] Step size.

``--local_theta ANGLE`` (default: 20)
    [LOCAL] Maximum angle between 2 steps.

``local_rk_order ORDER`` (default: 2)
    [LOCAL] Order of the Runge-Kutta integration.

``--local_min_len LENGTH`` (default: 3)
    [LOCAL] Minimum length.

``--local_max_len LENGTH`` (default: 15)
    [LOCAL] Maximum length.

``--local_compress_streamlines BOOL`` (default: true)
    [LOCAL] Compress streamlines.

``--local_compress_value THRESHOLD`` (default: 0.2)
    [LOCAL] Compression error threshold.
    See [Presseau et al Neuroimage 2015] and [Rheault et al Front Neuroinform 2017].

``--local_sfthres_init VALUE`` (default: 0.5)
    [LOCAL] Relative threshold value for the initial direction.

``--local_sfthres VALUE`` (default: 0.1)
    [LOCAL] Spherical function relative threshold.