Options ======= To display the options of Tractoflow, please use ``nextflow run tractoflow -r 2.4.4 --help``. Optional BIDS arguments ------------ ``--bidsignore "bids_ignore_path"`` (default: none) If you want to ignore some subjects/sessions/runs or some files, you can provide an extra bidsignore file. Check: https://github.com/bids-standard/bids-validator#bidsignore ``-clean_bids BOOL`` (default: false) If set, it will remove all the participants that are missing any information. ``--fs "freesurfer_output_folder"`` (default: none) If you want to run Tractoflow-ABS (Atlas Based Segmentation) combined with a BIDS structure input you need to have this argument. 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]. ``--max_dti_shell_value`` (default: 1200) Maximum shell threshold to be consider as a DTI shell (b <= 1200). This is the default behaviour to select DTI shells. ``--dti_shells`` Shells selected to compute the DTI metrics (generally b <= 1200). Please write them between quotes e.g. (--dti_shells "0 300 1000"). If selected, it will overwrite max_dti_shell_value. ``--min_fodf_shell_value`` (default: 700) Minimum shell threshold to be consider as a fODF shell (b >= 700). This is the default behaviour to select fODF shells. ``--fodf_shells`` Shells selected to compute the fODF metrics (generally b >= 700). Please write them between quotes e.g. (--fodf_shells "0 1000 2000"). If selected, it will overwrite min_fodf_shell_value. ``--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. ``--min_nvox MIN_NVOX_THRESHOLD`` (default: 300) Minimum number of voxels 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. Optional PFT Tracking arguments ------------ ``--run_pft_tracking BOOL`` (default: true). [PFT] Run Particle Filter Tracking (PFT) ``--pft_seeding_mask_type TYPE`` (default: wm) [PFT] Seeding mask type [wm, interface, fa]. ``--pft_fa_seeding_mask_threshold THRESHOLD`` (default: 0.1) [PFT] FA threshold for FA seeding mask. ``--pft_algo ALGO`` (default: prob) [PFT] Tracking algorithm [prob, det]. ``--pft_seeding SEEDING`` (default: npv) [PFT] Seeding type [npv, nt]. ``--pft_nbr_seeds NBRSEEDS`` (default: 10) [PFT] Number of seeds related to the seeding type param. ``--pft_step SIZE`` (default: 0.5) [PFT] Step size. ``--pft_theta ANGLE`` (default: 20) [PFT] Maximum angle between 2 steps. ``--pft_min_len LENGTH`` (default: 20) [PFT] Minimum length. ``--pft_max_len LENGTH`` (default: 200) [PFT] Maximum length. ``--pft_compress_streamlines BOOL`` (default: true) [PFT] Compress streamlines. ``--pft_compress_value THRESHOLD`` (default: 0.2) [PFT] Compression error threshold. See [Presseau et al Neuroimage 2015] and [Rheault et al Front Neuroinform 2017]. ``--pft_random_seed RANDOMSEED`` (default: 0) [PFT] List of random seed numbers for the random number generator. Please write them as list separated using commat WITHOUT SPACE e.g. (--pft_random_seed 0,1,2) Optional Local Tracking arguments ------------ ``--run_local_tracking BOOL`` (default: false). [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: 0.5) [LOCAL] Step size. ``--local_theta ANGLE`` (default: 20) [LOCAL] Maximum angle between 2 steps. ``--local_min_len LENGTH`` (default: 20) [LOCAL] Minimum length. ``--local_max_len LENGTH`` (default: 200) [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_random_seed RANDOMSEED`` (default: 0) [LOCAL] List of random seed numbers for the random number generator. Please write them as list separated using commat WITHOUT SPACE e.g. (--local_random_seed 0,1,2) ``--local_batch_size_gpu`` (default: 10000) [LOCAL-GPU] Approximate size of GPU batches (number of streamlines to track in parallel). ``--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.