Pipeline Parameters

Input/output options

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

Parameter	Description	Type	Default	Required	Hidden
`input`	Either a path to a BIDS database or to comma-separated file containing information about the input subjects files. Help BIDS database or csv file containing a list of subjects to process. See `assets/samplesheet.csv`.	`string`		True
`bids_config`	BIDS configuration file in json pre-generated by TractoFlow(Read_BIDS process). This option must be used only if loading bids from —input did not work due to an issue in the BIDS folder. Help BIDS configuration file in json pre-generated by TractoFlow(Read_BIDS process). This option must be used only if loading bids from —input did not work due to an issue in the BIDS folder.	`string`
`fsbids`	Freesurfer BIDS derivative to use to load segmentations and parcellations. Help Freesurfer BIDS derivative to use to load segmentations and parcellations.	`string`
`bidsignore`	If you want to ignore some subjects or some files, you can provide an extra bidsignore file. Check: https://github.com/bids-standard/bids-validator#bidsignore Help If you want to ignore some subjects or some files, you can provide an extra bidsignore file. Check: https://github.com/bids-standard/bids-validator#bidsignore	`string`
`clean_bids`	If set, it will remove all the participants that are missing any information. Help If set, it will remove all the participants that are missing any information.	`boolean`
`b0_thr_extract_b0`	Consider all b-values below threshold as b=0 images. Help Consider all b-values below threshold as b=0 images.	`integer`	10
`dwi_shell_tolerance`	Consider all b-values up to +-tolerance as belonging to the same shell. Help Consider all b-values up to +-tolerance as belonging to the same shell.	`integer`	20
`outdir`	The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. Help The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.	`string`		True
`clean_output`	The results will be saved in BIDS. Help Check BIDS derivatives.	`boolean`	True
`email`	Email address for completion summary. Help Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don’t need to specify this on the command line for every run.	`string`			True
`multiqc_title`	MultiQC report title. Printed as page header, used for filename if not otherwise specified. Help MultiQC report title. Printed as page header, used for filename if not otherwise specified.	`string`			True

DWI preprocessing options

All parameters related to DWI preprocessing.

Parameter	Description	Type	Default	Hidden
`bet_prelim_f`	Fractional Intensity threshold for preliminary brain masking. Help Fractional Intensity threshold for preliminary brain masking.	`number`	0.16
`dilate_b0_mask_prelim_brain_extraction`	Dilation radius applied to the preliminary mask to ensure whole brain coverage. Help Dilation radius applied to the preliminary mask to ensure whole brain coverage.	`integer`	5
`run_dwi_denoising`	Run dwi denoising. Help Run dwi denoising.	`boolean`	True
`extent`	Denoising block size. Rule: extent^3 >= number of directions. Help Denoising block size. Rule: extent^3 >= number of directions.	`integer`	7
`run_gibbs_correction`	RRun Gibbs correction. Help RRun Gibbs correction.	`boolean`
`run_topup`	Run Topup. Help Run Topup.	`boolean`	True
`encoding_direction`	Encoding direction of the DWI [x, y, z] Help Encoding direction of the DWI [x, y, z]	`string`	y
`readout`	Readout time Help Readout time	`number`	0.062
`config_topup`	Configuration file to use for Topup. Can either be a full path to a file or the name of a configuration file in Topup resources.	`string`	b02b0.cnf	True
`prefix_topup`	Output prefix to use for susceptibility filtering output filenames.	`string`	topup_results	True
`run_eddy`	Run Eddy. Help Run Eddy.	`boolean`	True
`eddy_cmd`	Command to use to run Eddy. Help Command to use to run Eddy.	`string`	eddy_cpu
`bet_topup_before_eddy_f`	Fractional Intensity threshold for intermediate brain masking on Topup corrected b0 images. Help Fractional Intensity threshold for intermediate brain masking on Topup corrected b0 images.	`number`	0.16
`use_slice_drop_correction`	If set, will use the slice drop correction option from Eddy. Help If set, will use the slice drop correction option from Eddy.	`boolean`	True
`bet_dwi_final_f`	Fractional Intensity threshold for final brain masking. Help Fractional Intensity threshold for final brain masking.	`number`	0.16
`fa_mask_threshold`	FA threshold to compute WM mask for normalization. Help FA threshold to compute WM mask for normalization.	`number`	0.4

T1 preprocessing options

All parameters related to T1 preprocessing.

Parameter	Description	Type	Default	Required	Hidden
`run_t1_denoising`	Run T1 denoising. Help Run T1 denoising.	`boolean`	True
`template_t1`	Path to the template for antsBrainExtraction. The folder must contain t1_template.nii.gz and t1_brain_probability_map.nii.gz. Defaults to the mni_152_sym_09c template directory delivered with the pipeline in the assets directory. Help Path to the template for antsBrainExtraction. The folder must contain t1_template.nii.gz and t1_brain_probability_map.nii.gz. Defaults to the mni_152_sym_09c template directory delivered with the pipeline in the assets directory.	`string`

Resampling options

Resampling options for DWI and anatomical volumes.

Parameter	Description	Type	Default
`run_resample_dwi`	Run resample DWI. Help Run resample DWI.	`boolean`	True
`dwi_resolution`	DWI resolution. Help DWI resolution.	`number`	1.0
`dwi_interpolation`	DWI interpolation method. Help DWI interpolation method	`string`	lin
`run_resample_t1`	Run resample T1. Help Run resample T1.	`boolean`	True
`t1_resolution`	T1 resolution. Help T1 resolution.	`number`	1.0
`t1_interpolation`	T1 interpolation method. Help T1 interpolation method.	`string`	lin

DWI processing options

All parameters related to DWI processing (SH, DTI, fODF).

Parameter	Description	Type	Default
`max_dti_shell_value`	Maximum shell threshold to be consider as a DTI shell. This is the default behavior to select DTI shells. Help Maximum shell threshold to be consider as a DTI shell. This is the default behavior to select DTI shells.	`integer`	1200
`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. Help 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.	`string`
`min_fodf_shell_value`	Minimum shell threshold to be consider as a fODF shell. This is the default behaviour to select fODF shells. Help Minimum shell threshold to be consider as a fODF shell. This is the default behaviour to select fODF shells.	`integer`	700
`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. Help 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.	`string`
`fa`	Initial FA threshold to compute the frf. Help Initial FA threshold to compute the frf.	`number`	0.7
`min_fa`	Minimum FA threshold to compute the frf. Help Minimum FA threshold to compute the frf.	`number`	0.5
`min_nvox`	Minimum number of voxels to compute the frf. Help Minimum number of voxels to compute the frf.	`integer`	300
`roi_radius`	Region of interest radius to compute the frf. Help Region of interest radius to compute the frf.	`integer`	20
`manual_frf`	Force a fiber response function. Supply as 3 values : —manual_frf “mean_b0 parallel_diff perpendicular_diff”. Help Force a fiber response function. Supply as 3 values : —manual_frf “mean_b0 parallel_diff perpendicular_diff”.	`string`	15,4,4
`mean_frf`	Average the frf of all subjects. USE ONLY IF ALL OF SUBJECTS COME FROM THE SAME SCANNER AND ADHERE TO THE SAME ACQUISITION PROTOCOL. Help Average the frf of all subjects. USE ONLY IF ALL OF SUBJECTS COME FROM THE SAME SCANNER AND ADHERE TO THE SAME ACQUISITION PROTOCOL.	`boolean`
`sh_order`	Spherical harmonics order, must be even. Rules : sh_order=8 for 45 directions, sh_order=6 for 28 directions. Help Spherical harmonics order, must be even. Rules : sh_order=8 for 45 directions, sh_order=6 for 28 directions.	`integer`	8
`basis`	fODF basis. Help fODF basis.	`string`	descoteaux07
`fodf_metrics_a_factor`	Multiplicative factor for AFD max in ventricles. Help Multiplicative factor for AFD max in ventricles.	`number`	2.0
`relative_threshold`	Relative threshold on fODF amplitude in ]0,1]. Help Relative threshold on fODF amplitude in ]0,1].	`number`	0.1
`max_fa_in_ventricle`	Maximal threshold of FA to be considered as ventricles voxels. Help Maximal threshold of FA to be considered as ventricles voxels.	`number`	0.1
`min_md_in_ventricle`	Minimal threshold of MD in mm2/s to be considered as ventricles voxels. Help Minimal threshold of MD in mm2/s to be considered as ventricles voxels.	`number`	0.003
`sh_fitting`	Compute a Spherical Harmonics fit on the DWI, and output the SH coefficients in a Nifti file. Help Compute a Spherical Harmonics fit on the DWI, and output the SH coefficients in a Nifti file.	`boolean`
`sh_fitting_basis`	SH basis used for the optional SH fitting. Help SH basis used for the optional SH fitting.	`string`	descoteaux07
`sh_fitting_order`	SH order used for the optional SH fitting, must be an even number. Rules : sh_order=8 for 45 directions, sh_order=6 for 28 directions Help SH order used for the optional SH fitting, must be an even number. Rules : sh_order=8 for 45 directions, sh_order=6 for 28 directions	`integer`	6
`sh_fitting_shells`	Shells selected to compute the SH fitting. Please write them between quotes e.g. (—sh_fitting_shells “0 1000”). NOTE: SH fitting works only on single shell. You must include the b0 shell as well. Help Shells selected to compute the SH fitting. Please write them between quotes e.g. (—sh_fitting_shells “0 1000”). NOTE: SH fitting works only on single shell. You must include the b0 shell as well.	`string`

Particle Filtering Tractography options

All parameters related to particle filtering tractography on fODF fields.

Parameter	Description	Type	Default	Hidden
`run_pft_tracking`	Run Particle Filtering Tractography (PFT). Help Run Particle Filtering Tractography (PFT).	`boolean`	True
`pft_seeding_mask_type`	[PFT] Seeding mask type. Help [PFT] Seeding mask type.	`string`	wm
`pft_fa_seeding_mask_threshold`	[PFT] FA threshold for FA seeding mask. Help [PFT] FA threshold for FA seeding mask.	`number`	0.1
`pft_algo`	[PFT] Tracking algorithm. Help [PFT] Tracking algorithm.	`string`	prob
`pft_seeding`	[PFT] Seeding type. Help [PFT] Seeding type.	`string`	npv
`pft_nbr_seeds`	[PFT] Number of seeds related to the seeding type param. Help [PFT] Number of seeds related to the seeding type param.	`integer`	10
`pft_step`	[PFT] Step size. Help [PFT] Step size.	`number`	0.5
`pft_theta`	[PFT] Maximum angle between 2 steps. Help [PFT] Maximum angle between 2 steps.	`number`	20.0
`pft_sfthres`	Threshold on spherical functions computed from fODF.	`number`	0.1	True
`pft_sfthres_init`	Initial threshold on spherical functions computed from fODF.	`number`	0.5	True
`pft_min_len`	[PFT] Minimum length. Help [PFT] Minimum length.	`number`	20.0
`pft_max_len`	[PFT] Maximum length . Help [PFT] Maximum length .	`number`	200.0
`pft_particles`	Number of particles propagated in case of premature termination.	`integer`	15	True
`pft_back`	Length of the backtracking steps of the particle filter in mm.	`number`	2.0	True
`pft_front`	Length of the forward tracking steps of the particle filter in mm.	`number`	1.0	True
`pft_compress_value`	[PFT] Compression error threshold. Help [PFT] Compression error threshold.	`number`	0.2
`pft_random_seed`	[PFT] List of random seed numbers for the random number generator. Please write them as list separated using comma WITHOUT SPACE e.g. (—pft_random_seed 0,1,2) Help [PFT] List of random seed numbers for the random number generator. Please write them as list separated using comma WITHOUT SPACE e.g. (—pft_random_seed 0,1,2)	`integer`	0

Local Tractography options

All parameters related to local tractography on fODF fields.

Parameter	Description	Type	Default	Hidden
`run_local_tracking`	Run Local Tracking. Help Run Local Tracking.	`boolean`	True
`local_seeding_mask_type`	[LOCAL] seeding mask type. Help [LOCAL] seeding mask type.	`string`	wm
`local_fa_seeding_mask_threshold`	[LOCAL] FA threshold for FA seeding mask. Help [LOCAL] FA threshold for FA seeding mask.	`number`	0.1
`local_tracking_mask_type`	[LOCAL] tracking mask type. Help [LOCAL] tracking mask type.	`string`	wm
`local_fa_tracking_mask_threshold`	[LOCAL] FA threshold for FA tracking mask. Help [LOCAL] FA threshold for FA tracking mask.	`number`	0.1
`local_algo`	[LOCAL] Tracking algorithm. Help [LOCAL] Tracking algorithm.	`string`	prob
`local_seeding`	[LOCAL] Seeding type. Help [LOCAL] Seeding type.	`string`	npv
`local_nbr_seeds`	[LOCAL] Number of seeds related to the seeding type param. Help [LOCAL] Number of seeds related to the seeding type param.	`integer`	10
`local_step`	[LOCAL] Step size. Help [LOCAL] Step size.	`number`	0.5
`local_theta`	[LOCAL] Maximum angle between 2 steps. Help [LOCAL] Maximum angle between 2 steps.	`number`	20.0
`local_sfthres`	Threshold on spherical functions computed from fODF.	`number`	0.1	True
`local_sfthres_init`	Initial threshold on spherical functions computed from fODF.	`number`	0.5	True
`local_min_len`	[LOCAL] Minimum length. Help [LOCAL] Minimum length.	`number`	20.0
`local_max_len`	[LOCAL] Maximum length. Help [LOCAL] Maximum length.	`number`	200.0
`local_compress_value`	[LOCAL] Compression error threshold. Help [LOCAL] Compression error threshold.	`number`	0.2
`local_random_seed`	[LOCAL] List of random seed numbers for the random number generator. Please write them as list separated using comma WITHOUT SPACE e.g. (—local_random_seed 0,1,2). Help [LOCAL] List of random seed numbers for the random number generator. Please write them as list separated using comma WITHOUT SPACE e.g. (—local_random_seed 0,1,2).	`integer`	0
`local_batch_size_gpu`	[LOCAL-GPU] Approximate size of GPU batches (number of streamlines to track in parallel). Help [LOCAL-GPU] Approximate size of GPU batches (number of streamlines to track in parallel).	`integer`	10000
`local_tracking_gpu`	Use GPU tracking	`boolean`		True

Institutional config options

Parameters used to describe centralised config profiles. These should not be edited.

Parameter	Description	Type	Default	Hidden
`custom_config_version`	Git commit id for Institutional configs.	`string`	master	True
`custom_config_base`	Base directory for Institutional configs. Help If you’re running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don’t need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.	`string`	https://raw.githubusercontent.com/nf-core/configs/master	True
`config_profile_name`	Institutional config name.	`string`		True
`config_profile_description`	Institutional config description.	`string`		True
`config_profile_contact`	Institutional config contact information.	`string`		True
`config_profile_url`	Institutional config URL link.	`string`		True

Generic options

Less common options for the pipeline, typically set in a config file.

Parameter	Description	Type	Default	Hidden
`version`	Display version and exit.	`boolean`		True
`publish_dir_mode`	Method used to save pipeline results to output directory. Help The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.	`string`	copy	True
`email_on_fail`	Email address for completion summary, only when pipeline fails. Help An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.	`string`		True
`plaintext_email`	Send plain-text email instead of HTML.	`boolean`		True
`max_multiqc_email_size`	File size limit when attaching MultiQC reports to summary emails.	`string`	25.MB	True
`monochrome_logs`	Do not use coloured log outputs.	`boolean`		True
`multiqc_config`	Custom config file to supply to MultiQC.	`string`		True
`multiqc_logo`	Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file	`string`		True
`multiqc_methods_description`	Custom MultiQC yaml file containing HTML including a methods description.	`string`		True
`validate_params`	Boolean whether to validate parameters against the schema at runtime	`boolean`	True	True
`pipelines_testdata_base_path`	Base URL or local path to location of pipeline test dataset files	`string`	https://raw.githubusercontent.com/nf-core/test-datasets/	True
`trace_report_suffix`	Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.	`string`		True

{}

Parameter	Type	Default	Hidden
`preproc_dwi_run_denoising`	`boolean`	True	True
`preproc_dwi_run_degibbs`	`boolean`		True
`topup_eddy_run_topup`	`boolean`	True	True
`topup_eddy_run_eddy`	`boolean`	True	True
`preproc_dwi_run_N4`	`boolean`	True	True
`preproc_t1_run_denoising`	`boolean`	True	True
`preproc_t1_run_N4`	`boolean`	True	True
`preproc_t1_run_synthbet`	`boolean`		True
`preproc_t1_run_ants_bet`	`boolean`	True	True
`preproc_t1_run_crop`	`boolean`	True	True
`preproc_dwi_run_resampling`	`boolean`	True	True
`preproc_t1_run_resampling`	`boolean`	True	True
`frf_average_from_data`	`boolean`		True
`run_pft`	`boolean`	True	True

BundleSeg options

Define the behaviour of the bundle_seg subworkflow.

Parameter	Description	Type	Default
`run_bundle_seg`		`boolean`	False
`atlas_directory`	Path to the BundleSeg atlas directory. Help Path to the BundleSeg atlas directory. If not set, the default bundle_seg atlas will automatically downloaded.	`string`
`run_synthmorph`	Use SynthMorph for registration instead of ANTs for BundleSeg. (Requires Freesurfer license) Help Use SynthMorph for registration instead of ANTs for BundleSeg. (Requires Freesurfer license)	`boolean`

Tractometry options

Define the behaviour of the tractometry subworkflow.

Parameter	Description	Type	Default	Required	Hidden
`run_tractometry`		`boolean`	False
`nb_points`	Number of points for tractometry. Help Number of points for tractometry.	`integer`	10

Other parameters

Parameter	Description	Type	Default
`run_noddi`	Compute NODDI maps. Help Compute NODDI maps.	`boolean`
`run_freewater`	Run Freewater Elimination and compute Freewater corrected metrics. Help Run Freewater Elimination and compute Freewater corrected metrics.	`boolean`
`average_diff_priors`	Average diffusivity priors across subjects. Help Average diffusivity priors across subjects.	`boolean`	True
`para_diff`	Average parallel diffusivity value. Help Average parallel diffusivity value. Specifying this will override automatically computed values.	`string`
`iso_diff`	Average isotropic diffusivity value. Help Average isotropic diffusivity value. Specifying this will override automatically computed values.	`string`
`perp_diff_min`	Minimum perpendicular diffusivity value. Help Minimum perpendicular diffusivity value. Specifying this will override automatically computed values.	`string`
`perp_diff_max`	Maximum perpendicular diffusivity value. Help Maximum perpendicular diffusivity value. Specifying this will override automatically computed values.	`string`
`run_qball`	Compute Q-Ball metrics. Help Compute Q-Ball metrics (gfa, nufo, odf, …).	`boolean`
`use_qball_for_tracking`	Use Q-Ball model for tractography instead of fODFs. Help Use Q-Ball model for tractography instead of fODFs.	`boolean`	False
`run_atlas_based_tractometry`	Run atlas-based tractometry using ROI masks obtained from IIT.	`boolean`	False
`atlas_iit_b0`	Path to the IIT mean B0 nifti image file. Help Path to the IIT mean B0 nifti image file.	`string`
`atlas_iit_bundle_masks_dir`	Path to the directory holding all IIT bundle (binary) masks nifti files. Help Path to the directory holding all IIT bundle (binary) masks nifti files.	`string`