Pipeline Parameters

Input/output options

Define where the pipeline should find input data and save output data.

Parameter	Description	Type	Default	Required	Hidden
input	Path to the input directory location. Help Ensure the data structure is respected. For more information, see the documentation	string		True
outdir	The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. Help For a detailed description of the output files, please see the documentation.	string	results_mouse

General options

Major options.

Parameter	Description	Type	Default	Required	Hidden
use_preqc	Set it to true, if you want to use the output of the preqc. Needs to be combined with profile run_qc	boolean	False
use_fodf	Set it to true if you want to fODF instead of QBall reconstruction.	boolean	False
processes		integer	10		True

Steps options

Options to skip specific steps of the pipeline.

Parameter	Description	Type	Default	Required	Hidden
run_denoising	Set it to false if you don’t want to denoise your data.	boolean	True
run_eddy	Set it to false if you don’t want to use eddy correction.	boolean	True
run_n4	Set it to false if you don’t want to use N4.	boolean	True
run_resampling	Set it to false if you don’t want to resample your data to the smallest current voxel dimension.	boolean	True
run_tracking	Set it to false if you don’t want to run tractography.	boolean	True

Reconstruction options

Options for the FODF/QBall reconstruction step.

Parameter	Description	Type	Default	Required	Hidden
b0_threshold	Min b-value to considered as b0.	integer	100		True
shell_tolerance	The tolerated gap between the b-values to extract and the actual b-values.	integer	100		True
max_dti_shell_value	Maximum DTI shell value used.	integer	3500		True
nvox_min	Minimum number of voxels to include in the computation of the FRF.	integer	100		True
sh_order	Spherical harmonics order used in the FODF/QBall processing step.	integer	6		True

Tracking options

Options specific to the tracking algorithm.

Parameter	Description	Type	Default	Required	Hidden
local_nbr_seeds	Number of seeds used in the local tracking step.	integer	1		True
local_step_pct	Percentage step value used in the local tracking step.	number	50		False
local_theta	Theta value used in the local tracking step.	number	45		True
local_rk_order	The order of the Runge-Kutta integration used for the step function.	integer	1		True
local_min_len	Minimum length used in the local tracking step (mm).	integer	3		True
local_max_len	Maximum length used in the local tracking step (mm).	integer	12		True