Pipeline Parameters

Input/output options

This section will detail how to set the inputs and outputs of the pipeline.

Parameter	Description	Type	Required	Hidden
`input`	Path to the BIDS directory location. Help Ensure the BIDS data structure is respected. For more information, see the documentation	`string`
`participant_label`	List of participant IDs or a single participant ID. Help This will be used to select the specific participants to process. The best way to provide them is in a params.yml file, see the documentation for more information.	`array`
`input_deriv`	Path to the derivatives directory to use as input.	`string`
`bids_script`	Path to the BIDS script. Help This is a script that will be used to generate the BIDS directory structure from the raw data. Unless you know what you are doing, this should not be changed. Will be removed in a future release.	`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`	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`
`multiqc_title_subject`	MultiQC report title for subject report. Printed as page header, used for filename if not otherwise specified.	`string`
`multiqc_title_global`	MultiQC report title for global report. Printed as page header, used for filename if not otherwise specified.	`string`

Segmentation Options

Options for FreeSurfer, FastSurfer, and/or M-CRIB-S processing. Only relevant if you select the segmentation profile.

Parameter	Description	Type	Default	Hidden
`method`	Method to use to perform surface reconstruction and cortical/subcortical segmentation. Will only affect subjects > 3 months of age. Recon-all-clinical is highly recommended for subjects between 3 months and 5 years old. Options include recon-all, recon-all-clinical, or FastSurfer.	`string`	recon-all-clinical	False
`fs_license`	Path to FreeSurfer license file. Help This is required to run the segmentation profile. You can obtain a FreeSurfer license from the FreeSurfer website here.	`string`
`cerebnet`	Use CerebNet for cerebellum segmentation in FastSurfer.	`boolean`	False	True
`hypvinn`	Use HypVINN for hypothalamus sub-segmentation in FastSurfer.	`boolean`	False	True
`acq3T`	Use 3T acquisition parameters.	`boolean`	True	True
`fs_output_dir`	Path to FreeSurfer/FastSurfer/M-CRIB-S output directory. Help Default location will be alongside `--outdir`. For more information, please see the documentation	`string`		False
`mcribs_jointhresh`	Join threshold used in the MCRIBS surface reconstruction step.	`number`		True
`mcribs_fastcollision`	Use deformable fast collision test in the MCRIBS surface reconstruction step.	`boolean`	False	True
`mcribs_nopialoutside`	Do not ensure pial is outside of WM in the MCRIBS surface reconstruction step.	`boolean`	False	True
`mcribs_seed`	Seed used in the MCRIBS surface reconstruction step.	`number`	1234	True

Atlases Options

Options for atlases used in the pipeline.

Parameter	Description	Type	Default	Required	Hidden
`utils_folder`	Path to the utils folder. Help This folder contains the atlases used in the pipeline. Unless you know what you are doing, please do not change this.	`string`			True

Processing steps to apply on anatomical images.

Processing steps to apply on anatomical images. (NOTE: the same steps will be applied on both T1w/T2w if both are available).

Parameter	Description	Type	Default	Hidden
`preproc_run_denoising`	Run denoising on the anatomical images.	`boolean`	True	False
`preproc_run_N4`	Run N4 bias correction on the anatomical images.	`boolean`	True	False
`preproc_run_resampling`	Run resampling on the anatomical images.	`boolean`	True	False
`preproc_run_synthstrip`	Run SynthStrip for brain extraction.	`boolean`	True	False
`preproc_run_ants_bet`	Run AntsBet for brain extraction Help This step will require the use of a template image which does not match all ages and is much slower than the default synthstrip method. Not recommended.	`boolean`	False	False
`preproc_run_crop`	Run cropping on the anatomical images.	`boolean`	True	False
`synthstrip_weights`	Path to alternative weights for SynthStrip brain extraction.	`string`	None	False

T1w Processing Options

Options for T1w processing. In the case where you do not have a T1w image, you can ignore those options.

Parameter	Description	Type	Default	Hidden
`t1_denoise_number_of_coils`	Number of coils used in the T1w denoising step.	`integer`	1	True
`t1_bias_bspline_knot_per_voxel`	Number of B-spline knots per voxel used in the T1w bias correction step.	`number`	8	True
`t1_bias_shrink_factor`	Shrink factor used in the T1w bias correction step.	`integer`	4	True
`t1_resample_voxel_size`	Voxel size used in the T1w resampling step.	`integer`	1	True
`t1_resample_interp`	Interpolation method used in the T1w resampling step.	`string`	lin	True
`t1_synthstrip_border`	Mask border threshold used in the SynthStrip brain extraction step.	`integer`	1	True
`t1_synthstrip_nocsf`	Exclude CSF from the border in the SynthStrip brain extraction step.	`boolean`	False	True

T2w Preprocessing Options

Options for T2w preprocessing. In the case where you do not have a T2w image, you can ignore those options.

Parameter	Description	Type	Default	Hidden
`t2_denoise_number_of_coils`	Number of coils used in the T2w denoising step.	`integer`	1	True
`t2_bias_bspline_knot_per_voxel`	Number of B-spline knots per voxel used in the T2w bias correction step.	`number`	8	True
`t2_bias_shrink_factor`	Shrink factor used in the T2w bias correction step.	`integer`	4	True
`t2_resample_voxel_size`	Voxel size used in the T2w resampling step.	`integer`	1	True
`t2_resample_interp`	Interpolation method used in the T2w resampling step.	`string`	lin	True
`t2_synthstrip_border`	Mask border threshold used in the SynthStrip brain extraction step.	`integer`	1	True
`t2_synthstrip_nocsf`	Exclude CSF from the border in the SynthStrip brain extraction step.	`boolean`	False	True

Anatomical Co-registration Options

Options for anatomical co-registration. Will only be performed if both T2w and T1w images are available.

Parameter	Description	Type	Default	Hidden
`coreg_dimensionality`	Dimensionality of the registered images.	`integer`	3	True
`coreg_transform`	Transform used in the coregistration step. t: translation (1 stage), r: rigid (1 stage), a: rigid + affine (2 stages), s: rigid + affine + deformable syn (3 stages)	`string`	a	False
`coreg_quick`	Use antsRegistrationSyNQuick for the coregistration step.	`boolean`	False	False

DWI Preprocessing Options

Options for DWI preprocessing. You can use these options to customise the behaviour of the DWI preprocessing steps.

Parameter	Description	Type	Default	Hidden
`skip_dwi_preprocessing`	Skip the DWI preprocessing steps.	`boolean`	False	False
`dwi_b0_threshold`	B0 threshold used in the DWI preprocessing steps.	`integer`	20	False
`dwi_shell_tolerance`	Shell tolerance used in the DWI preprocessing steps.	`integer`	50	False
`preproc_dwi_run_denoising`	Run denoising on the DWI images.	`boolean`	True	False
`dwi_denoise_patch_size`	Patch size used in the DWI denoising step.	`integer`	7	True
`preproc_dwi_run_degibbs`	Run Gibbs ringing correction on the DWI images.	`boolean`	False	False
`topup_eddy_run_topup`	Run topup in the susceptibility distortion correction step.	`boolean`	True	False
`dwi_susceptibility_config_file`	Path to the susceptibility distortion correction config file.	`string`	b02b0.cnf	True
`dwi_susceptibility_output_prefix`	Prefix used in the susceptibility distortion correction step.	`string`	topup_results	True
`dwi_susceptibility_readout`	Readout time used in the susceptibility distortion correction step.	`number`	0.04	True
`dwi_susceptibility_encoding_dir`	Encoding direction used in the susceptibility distortion correction step.	`string`	y	True
`topup_eddy_run_eddy`	Run eddy in the eddy current correction step.	`boolean`	True	False
`dwi_motion_and_eddy_command`	Command used in the motion and eddy correction step.	`string`	eddy_cpu	True
`dwi_motion_and_eddy_bet_f_threshold`	Bet f threshold used in the motion and eddy correction step.	`number`	0.16	True
`dwi_motion_and_eddy_restore_slices`	Restore slices in the motion and eddy correction step.	`boolean`	True	True
`dwi_pwdavg_shells`	Shells used in the PowderAverage step.	`string`		False
`dwi_run_synthstrip`	Run SynthStrip for brain extraction	`boolean`	True	False
`dwi_synthstrip_border`	Brain border used in the SynthStrip brain extraction step.	`integer`	1	True
`dwi_synthstrip_nocsf`	Exclude CSF from the border in the SynthStrip brain extraction step.	`boolean`	False	True
`dwi_synthstrip_weights`	Alternative weights used in the SynthStrip brain extraction step.	`string`	None	False
`dwi_bet_f_threshold`	Bet f threshold used in the brain extraction step.	`number`	0.16	True
`preproc_dwi_run_N4`	Run N4 bias correction on the DWI images.	`boolean`	True	False
`dwi_bias_bspline_knot_per_voxel`	Number of B-spline knots per voxel used in the DWI bias correction step.	`number`	8	True
`dwi_bias_shrink_factor`	Shrink factor used in the DWI bias correction step.	`integer`	4	True
`dwi_normalize_fa_mask_threshold`	FA mask threshold used in the normalization step.	`number`	0.4	False
`preproc_dwi_run_resampling`	Run resampling on the DWI images.	`boolean`	True	False
`dwi_resample_voxel_size`	Voxel size used in the DWI resampling step.	`integer`	1	True
`dwi_resample_interp`	Interpolation method used in the DWI resampling step.	`string`	lin	True
`dwi_resample_mask_voxel_size`	Voxel size used in the DWI mask resampling step.	`integer`	1	True
`dwi_resample_mask_interp`	Interpolation method used in the DWI mask resampling step.	`string`	nn	True

DTI Options

Options for diffusion tensor fitting.

Parameter	Description	Type	Default	Required	Hidden
`dti_max_shell_value`	Maximum shell value used in the DTI processing step.	`integer`	1600		True
`dti_shells`	Shells used in the DTI processing step.	`string`			False

FRF Options

Options for fiber response function (FRF) processing. The FRF is derived from normative curves in function of each participant’s age. The current options are mostly if you want to override this default behavior.

Parameter	Description	Type	Default	Hidden
`frf_fa`	Minimum FA threshold to use to compute the FRF.	`number`	0.7	True
`frf_min_fa`	Minimum FA threshold to use to compute the FRF.	`number`	0.5	True
`frf_nvox_min`	Minimum number of voxels to include in the computation of the FRF.	`integer`	300	True
`frf_roi_radius`	Radius of the ROI used to compute the FRF.	`integer`	20	True
`frf_max_dti_shell_value`	Maximum DTI shell value used.	`integer`	1600	True
`frf_min_fodf_shell_value`	Minimum FODF shell value used.	`integer`	700	True
`frf_set_method`	Method used to compute the FRF.	`string`	ssst	False
`frf_manual_frf`	Manual FRF values.(e.g. ‘15,4,4’). This is set from the normative curves. Use this option only to apply a single FRF to every participants. For more information, please see the documentation.	`string`		False

FODF Options

Options for FODF processing.

Parameter	Description	Type	Default	Hidden
`fodf_min_fodf_shell_value`	Minimum FODF shell value used.	`integer`	700	True
`fodf_shells`	Shells used in the FODF processing step.	`string`		False
`fodf_sh_order`	Spherical harmonics order used in the FODF processing step.	`integer`	8	False
`fodf_sh_basis`	Spherical harmonics basis used in the FODF processing step. Choices: descoteaux07 or tournier07.	`string`	descoteaux07	False
`fodf_set_method`	Method used to compute the FODF.	`string`	ssst	False
`fodf_relative_threshold`	Relative threshold used in the FODF processing step.	`number`	0.1	True
`fodf_a_factor`	FODF a factor used in the FODF processing step.	`number`	2.0	True
`fodf_max_fa_threshold`	Maximum FA threshold used in the FODF processing step.	`number`	0.1	True
`fodf_min_md_threshold`	Minimum MD threshold used in the FODF processing step.	`number`	0.003	True

PFT Tracking Options

Options for Particle Filter Tracking (PFT).

Parameter	Description	Type	Default	Hidden
`run_pft_tracking`	Run PFT tracking.	`boolean`	True	False
`pft_seeding_mask_type`	Seeding mask type used in the PFT tracking step. Choices: wm, fa, or interface.	`string`	wm	False
`pft_fa_threshold`	FA threshold to use on FA map to generate seeding mask.	`number`	0.2	True
`pft_random_seed`	Random seed used in the PFT tracking step.	`integer`	1234	True
`pft_compress`	If true, compress the streamlines.	`boolean`	True	True
`pft_compress_value`	Compression value for the streamlines’ compression.	`number`	0.2	True
`pft_algo`	Algorithm used in the PFT tracking step. Choices: prob or det	`string`	prob	False
`pft_nbr_seeds`	Number of seeds used in the PFT tracking step.	`integer`	10	False
`pft_seeding_type`	Seeding type used in the PFT tracking step. Choices: npv or nt.	`string`	npv	False
`pft_step`	Step value used in the PFT tracking step.	`number`	0.5	True
`pft_theta`	Theta value used in the PFT tracking step.	`number`	20	True
`pft_sfthres`	SF threshold used in the PFT tracking step.	`number`	0.1	True
`pft_sfthres_init`	Initial SF threshold used in the PFT tracking step.	`number`	0.5	True
`pft_min_len`	Minimum length used in the PFT tracking step.	`number`	20	False
`pft_max_len`	Maximum length used in the PFT tracking step.	`number`	200	False
`pft_particles`	Number of particles used in the PFT tracking step.	`integer`	15	True
`pft_back`	Length of PFT back tracking (mm)	`integer`	2	True
`pft_front`	Length of PFT forward tracking (mm).	`integer`	1	True

Local Tracking Options

Options for local tracking.

Parameter	Description	Type	Default	Hidden
`run_local_tracking`	Run local tracking.	`boolean`	True	False
`local_seeding_mask_type`	Seeding mask type used in the local tracking step.	`string`	wm	False
`local_fa_tracking_mask_threshold`	FA threshold used for the tracking mask.	`number`	0.4	True
`local_fa_seeding_mask_threshold`	FA threshold used for the seeding mask.	`number`	0.4	True
`local_tracking_mask_type`	Tracking mask type used in the local tracking step. Choices: wm, fa, or interface.	`string`	wm	False
`local_random_seed`	Random seed used in the local tracking step.	`integer`	1234	True
`local_compress`	If true, compress the streamlines.	`boolean`	True	True
`local_compress_value`	Compression value for the streamlines’ compression.	`number`	0.2	True
`local_algo`	Algorithm used in the local tracking step. Choices: prob or det	`string`	prob	False
`local_nbr_seeds`	Number of seeds used in the local tracking step.	`integer`	10	False
`local_seeding_type`	Seeding type used in the local tracking step. Choices: npv or nt.	`string`	npv	False
`local_step`	Step value used in the local tracking step.	`number`	0.5	True
`local_theta`	Theta value used in the local tracking step.	`number`	20	True
`local_sfthres`	SF threshold used in the local tracking step.	`number`	0.1	True
`local_min_len`	Minimum length used in the local tracking step.	`number`	20	False
`local_max_len`	Maximum length used in the local tracking step.	`number`	200	False

BundleSeg Options

Options for BundleSeg

Parameter	Description	Type	Default	Hidden
`minimal_vote_ratio`	Ratio of vote across models to consider a streamline for saving. If you have 5 input models and a ratio of 0.5, you will need at least 3 votes.	`number`	0.5	False
`outlier_alpha`	Percentage of the length of the tree that clusters of individual streamlines will be pruned. Higher values will remove more streamlines.	`number`	0.6	False
`nb_points`	Number of points to segment the bundles.	`integer`	5	False
`colormap`	Colormap to use for coloring the bundles. Color only affects visualization.	`string`	jet	False
`density_weighting`	If set, weight statistics based on the number of voxel going through the voxel.	`boolean`	True	False
`normalize_weights`	If set, the weights will be normalized to the [0,1] range.	`boolean`	True	False
`length_stats`	If set, will output bundles’ length.	`boolean`	True	False
`endpoints_stats`	If set, will output statistics in endpoints.	`boolean`	True	False
`means_std`	If set, will output mean and std values per bundle per metrics.	`boolean`	True	False
`volume`	If set, will output volume values per bundle.	`boolean`	True	False
`streamline_count`	If set, will output the streamline count per bundle.	`boolean`	True	False
`volume_per_labels`	If set, will output volume values per labels per bundle.	`boolean`	True	False
`mean_std_per_point`	If set, will output mean and std per points per metrics per bundle.	`boolean`	True	False

Transform Labels Options

Options for transforming labels from anatomical to diffusion space.

Parameter	Description	Type	Default	Hidden
`labels_transform_dimensionality`	Dimensionality of the label file.	`integer`	3	True
`labels_output_suffix`	Name to use as suffix in the output filename.	`string`	_labels	True
`labels_interpolation`	Interpolation method used in the label transformation step. Choices: NearestNeighbor, Linear, or BSpline.	`string`	NearestNeighbor	True
`labels_output_dtype`	Output data type used in the label transformation step. Choices: float or int.	`string`	int	True

COMMIT Options

Options for COMMIT filtering.

Parameter	Description	Type	Default	Hidden
`run_commit2`	Run COMMIT2 filtering.	`boolean`	True	False
`commit2_lambda`	Lambda value used in the COMMIT filtering step.	`number`	0.001	True
`commit_para_diff`	Para diff value used in the COMMIT filtering step. Help This value is derived from normative curves in function of each participant’s age. For more information, please see the documentation.	`string`		False
`commit_iso_diff`	Iso diff value used in the COMMIT filtering step. Help This value is derived from normative curves in function of each participant’s age. For more information, please see the documentation.	`string`		False
`commit_perp_diff`	Perp diff value used in the COMMIT filtering step. Help This value is derived from normative curves in function of each participant’s age. For more information, please see the documentation.	`string`		False
`commit_ball_stick`	Use the ball and stick model in the COMMIT filtering step.	`boolean`	False	True
`commit_nbr_dir`	Number of directions used in the COMMIT filtering step.	`integer`	500	True

Decompose Tractogram Options

Options for decomposing the tractogram according to a label file.

Parameter	Description	Type	Default	Hidden
`decompose_no_pruning`	Do not prune the tractogram.	`boolean`	False	True
`decompose_no_remove_loops`	Do not remove loops from the tractogram.	`boolean`	False	True
`decompose_no_remove_outliers`	Do not remove outliers from the tractogram.	`boolean`	False	True
`decompose_no_remove_curv`	Do not remove curvilinear structures from the tractogram.	`boolean`	False	True
`decompose_min_len`	Minimum length used in the tractogram decomposition step.	`number`	20	False
`decompose_max_len`	Maximum length used in the tractogram decomposition step.	`number`	200	False
`decompose_outlier_threshold`	Outlier threshold used in the tractogram decomposition step.	`number`	0.6	False
`decompose_max_angle`	Maximum angle used in the tractogram decomposition step.	`number`	330.0	False
`decompose_max_curv`	Maximum curvature used in the tractogram decomposition step.	`number`	10.0	False

AFD Fixel Options

Options for AFD fixel processing.

Parameter	Description	Type	Default	Required	Hidden
`afd_fixel_length_weighting`	Use length weighting in the AFD fixel processing step.	`boolean`	False		True

Output to Template Options

Options for outputting to specific template space.

Parameter	Description	Type	Default	Hidden
`template`	Template space to output to. The available template are the ones supported by TemplateFlow, please see their documentation for an exhaustive list (https://www.templateflow.org/browse/).	`string`	None	False
`templateflow_res`	Resolution of the template space.	`integer`	1	False
`templateflow_cohort`	Cohort to use for the template space (not required for most template, but if it is, simply provide the cohort’s number).	`integer`		False
`templateflow_home`	Path to the TemplateFlow home directory where templates will be downloaded. If you are running the pipeline without internet access, this needs to point to a folder containing predownloaded templates.	`string`	./templateflow	False
`use_template_t2w`	Use the T2w image from the template space (useful with infant data.).	`boolean`	False	False

Pipeline profile

Pipeline profile options. This is a short list of options. For full description, please see the documentation

Parameter	Description	Type	Default	Hidden
`tracking`	Perform tracking profile.	`boolean`	False	True
`bundling`	Perform bundle extraction profile.	`boolean`	False	True
`connectomics`	Perform connectomics profile.	`boolean`	False	True
`segmentation`	Perform segmentation profile.	`boolean`	False	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
`lean_output`	Do not copy intermediate files to output directory.	`boolean`		False
`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
`hook_url`	Incoming hook URL for messaging service Help Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.	`string`		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`
`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`	None	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