Options

To display the options of Tractoflow, please use nextflow run tractoflow -r 2.4.0 --help.

Optional BIDS arguments

--participants_label "SUBID1 SUBID2" (default: none)

The label(s) of the specific participant(s) you want to analyzed. It does not include “sub-“. Please write one or more subjects between quotes e.g. (–participants_label “01 02 04”) If this parameter is not provided all subjects should be analyzed

-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)

--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.