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.

--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.