Options¶
To display the options of Tractoflow, please use
nextflow run tractoflow/main.nf --help
.
Options list¶
--b0_thr_extract_b0 MAX_VALUE
(default: 10)- 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.
--bet_prelim_f THRESHOLD
(default: 0.16)- Fractional Intensity threshold (-f for the bet FSL command) for preliminary DWI brain extraction. See FSL bet documentation for more info.
--dilate_b0_mask_prelim_brain_extraction FACTOR
(default: 5)- Dilation factor to keep the whole brain and be more robust to the geometric distortions. This is only applied to the preliminary BET. Not the final extraction.
--run_dwi_denoising BOOL
(default: true)- Run dwi denoising (dwidenoise from Mrtrix3). See Mrtrix3 dwidenoise documentation for more info.
--extent SIZE
(default: 7)- Denoising block size. Recommended block size should follow the following rule of thumb: extent^3 >= # directions. See Mrtrix3 dwidenoise documentation for more info.
--run_topup BOOL
(default: true)- Run Topup. If TractoFlow find any reversed phase encoded b=0 images. Topup will be automatically ignored. See FSL Topup documentation for more info.
--encoding_direction DIRECTION
(default: y)- Encoding direction of the DWI [x, y, z]. See FSL Topup documentation for more info.
--readout VALUE
(default: 0.062)- Readout time value.
--run_eddy BOOL
(default: true)- Run Eddy.
--eddy_cmd COMMAND
(default: eddy_openmp)- Eddy command to use [eddy_openmp, eddy_cuda].
--bet_topup_before_eddy_f THRESHOLD
(default: 0.16)- Fractional Intensity threshold (-f for the bet FSL command) for intermediate BET operation on topup corrected images.
--use_slice_drop_correction BOOL
(default: true)- If set, will use the slice drop correction option (–repol) from Eddy.
--bet_dwi_final_f THRESHOLD
(default: 0.16)- Fractional Intensity threshold (-f for the bet FSL command) for the final DWI BET.
--fa_mask_threshold THRESHOLD
(default: 0.4)- FA maximum value to be considered as WM for Normalize DWI.
--run_resample_dwi BOOL
(default: true)- Run resample DWI. Resampling is done at the resolution given by –dwi_resolution option.
--dwi_resolution RESOLUTION
(default: 1)- DWI resolution (in mm).
--dwi_interpolation METHOD
(default: lin)- Interpolation method [nn, lin, quad, cubic].
--run_t1_denoising BOOL
(default: true)- Run T1 denoising using NLmean algorithm.
--run_resample_t1 BOOL
(default: true)- Run resample T1. Resampling is done at the resolution given by –t1_resolution option.
--t1_resolution RESOLUTION
(default: 1)- T1 resolution (in mm).
--t1_interpolation METHOD
(default: lin)- Interpolation method [nn, lin, quad, cubic].
--number_of_tissues NUMBER
(default: 3)- Number of tissue classes (-n for the fast FSL command).
--fa THRESHOLD
(default: 0.7)- Initial FA threshold to compute the fiber response function (FRF).
--min_fa MIN_THRESHOLD
(default: 0.5)- Minimum FA threshold to compute the FRF.
--roi_radius RADIUS
(default: 20)- Region of interest radius to compute the FRF. This ROI starts from the center of the 3D volume (sizeX/2, sizeY/2, sizeZ/2).
--set_frf BOOL
(default: false)- Set manually the FRF.
--manual_frf FRF
(default: “15,4,4”)- FRF set manually. The FRF must be at 10^-4 scaling in mm^2/s. This corresponds to an elongated symmetric diffusion tensor with eigenvalues (15, 4, 4) x 10^-4 mm^2/s along the principal axis and radial axes respectively.
--mean_frf BOOL
(default: true)- Mean the frf of all subjects. USE ONLY IF ALL OF SUBJECTS COME FROM THE SAME SCANNER AND HAVE THE SAME ACQUISITION.
--sh_order ORDER
(default: 8)Spherical harmonics order.
Suggested rule of thumb :–sh_order=8 for 45+ directions–sh_order=6 for 20+ directions–sh_order=4 otherwise--basis BASIS
(default: descoteaux07)- fODF spherical harmonics (SH) basis type [descoteaux07, tournier07].
--fodf_metrics_a_factor FACTOR
(default: 2.0)- Multiplicative factor for AFD max in ventricles. As recommended in [Dell’Acqua et al HBM 2013].
--relative_threshold THRESHOLD
(default: 0.1)- Relative threshold on fODF amplitude in ]0,1].
--max_fa_in_ventricle THRESHOLD
(default: 0.1)- Maximal threshold of FA to be considered as ventricule voxel. Used to compute the ventricules mask and find the maximum fODF amplitude in the ventricules.
--min_md_in_ventricle THRESHOLD
(default: 0.003)- Minimal threshold of MD in mm^2/s to be considered as ventricule voxel. Used to compute the ventricules mask and find the maximum fODF amplitude in the ventricules.
--wm_seeding BOOL
(default: true)- If ‘–wm_seeding true’, use the WM-GM interface and the WM mask as seeding mask, else use the WM-GM interface as seeding mask.
--algo ALGO
(default: prob)Tracking algorithm [prob, det].
prob: streamline probabilistic.det: streamline deterministic.--seeding TYPE
(default: npv)Seeding type [npv, nt].
npv: number of seeds per voxel of the seeding masknt: total number of seeds randomly placed in the seeding mask--nbr_seeds NUMBER
(default: 10)- Number of seeds related to the seeding type param.
--random SEED
(default: 0)- Random seed. Fixed for reproducible seeds
--step SIZE
(default: 0.5)- Step size in mm.
--theta ANGLE
(default: 20)- Maximum angle between 2 steps in degrees.
--min_len LENGTH
(default: 20)- Minimum length in mm.
--max_len LENGTH
(default: 200)- Maximum length in mm.
--compress_streamlines BOOL
(default: true)- Compress streamlines.
--compress_value THRESHOLD
(default: 0.2)- Compression error threshold in mm. See [Presseau et al Neuroimage 2015] and [Rheault et al Front Neuroinform 2017]
--template_t1 PATH
(default: /human-data/mni_152_sym_09c/t1)- Path to the template T1 directory for antsBrainExtraction. The folder must contain t1_template.nii.gz and t1_brain_probability_map.nii.gz. The default path is the human_data folder in the Singularity/Docker container.
--processes_brain_extraction_t1 NUMBER
(default: 4)- Number of processes for T1 brain extraction task.
--processes_denoise_dwi NUMBER
(default: 4)- Number of processes for DWI denoising task.
--processes_denoise_t1 NUMBER
(default: 4)- Number of processes for T1 denoising task.
--processes_eddy NUMBER
(default: 1)- Number of processes for eddy task.
--processes_fodf NUMBER
(default: 4)- Number of processes for fODF task.
--processes_registration NUMBER
(default: 4)- Number of processes for registration task.
--output_dir PATH
(default: ./results)- Directory where to write the final results.
--processes NUMBER
(default: Maximum number of threads)- The number of parallel processes to launch. Only affects the local scheduler.