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	False
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
participants_tsv	Path to the participants.tsv file. Help Path to the participants.tsv file. If this is not specified, the participants.tsv file will be fetched automatically if the input is a BIDS directory, otherwise no additional covariates will be used.	string
participant_label	Comma-separated list of participant labels include in the processing. If specified, only these participants will be processed (unless excluded by ‘exclude_participant_label’). Help Comma-separated list of participant labels include in the processing. If specified, only these participants will be processed (unless excluded by ‘exclude_participant_label’).	string
exclude_participant_label	Comma-separated list of prefixes to exclude from the processing. If specified, participants with labels starting with any of these prefixes will be excluded from processing. Help Comma-separated list of prefixes to exclude from the processing. If specified, participants with labels starting with any of these prefixes will be excluded from processing.	string
help	Display the help message.	['boolean', 'string']
help_full	Display the full detailed help message.	boolean	False
show_hidden	Display hidden parameters in the help message (only works when —help or —help_full are provided).	boolean	False

DWI preprocessing options

All parameters related to DWI preprocessing.

Parameter	Description	Type	Default	Required	Hidden
keep_dwi_with_skull	Keep DWI in native space with skull when reconstructing local models and tractograms. Help Keep DWI in native space with skull when reconstructing local models and tractograms.	boolean	False
run_dwi_synthstrip	Run Synthstrip for BET DWI. Help Run Synthstrip for BET DWI.	boolean	False
synthstrip_weights	Path to the Synthstrip weights to use for BET DWI and BET T1. If not provided, default weights will be used. Help Path to the Synthstrip weights to use for BET DWI and BET T1. If not provided, default weights will be used.	string	None
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	Run Gibbs correction. Help Run Gibbs correction.	boolean	True
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. (accepted: eddy_cpu|eddy_cuda10.2|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
run_dwi_N4	Run DWI N4 bias correction. Help Run DWI N4 bias correction.	boolean	True
run_dwi_normalize	Run DWI normalization. Help Run DWI normalization.	boolean	True
run_qball	Compute Q-Ball metrics. Help Compute Q-Ball metrics (gfa, nufo, odf, …).	boolean	False
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

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
run_t1_N4	Run T1 N4 bias correction. Help Run T1 N4 bias correction.	boolean	True
run_t1_crop	Run T1 cropping. Help Run T1 cropping.	boolean	True
run_t1_ants_bet	Run T1 brain extraction using ANTs. Help Run T1 brain extraction using ANTs.	boolean	True
run_t1_synthstrip	Run T1 brain extraction using Synthstrip. Help Run T1 brain extraction using Synthstrip.	boolean	False
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	Required	Hidden
run_dwi_resampling	Run resample DWI. Help Run resample DWI.	boolean	True
dwi_resolution	DWI resolution. Help DWI resolution.	number	1.0
dwi_interpolation	DWI interpolation method. (accepted: nn|lin|quad|cubic) Help DWI interpolation method	string	lin
run_t1_resampling	Run resample T1. Help Run resample T1.	boolean	True
t1_resolution	T1 resolution. Help T1 resolution.	number	1.0
t1_interpolation	T1 interpolation method. (accepted: nn|lin|quad|cubic) Help T1 interpolation method.	string	lin

DWI processing options

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

Parameter	Description	Type	Default	Required	Hidden
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. (accepted: descoteaux07|tournier07) 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	False
sh_fitting_basis	SH basis used for the optional SH fitting. (accepted: descoteaux07|tournier07) 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	Required	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. (accepted: wm|interface|fa) 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. (accepted: prob|det) Help [PFT] Tracking algorithm.	string	prob
pft_seeding	[PFT] Seeding type. (accepted: npv|nt) 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	Required	Hidden
run_local_tracking	Run Local Tracking. Help Run Local Tracking.	boolean	True
local_seeding_mask_type	[LOCAL] seeding mask type. (accepted: wm|fa|interface) 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. (accepted: wm|fa) 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. (accepted: prob|det) Help [LOCAL] Tracking algorithm.	string	prob
local_seeding	[LOCAL] Seeding type. (accepted: npv|nt) 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	False		True

Institutional config options

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

Parameter	Description	Type	Default	Required	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	Required	Hidden
version	Display version and exit.	boolean	False		True
publish_dir_mode	Method used to save pipeline results to output directory. (accepted: symlink|rellink|link|copy|copyNoFollow|move) 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	False		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	False		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

BundleSeg options

Define the behaviour of the bundle_seg subworkflow.

Parameter	Description	Type	Default	Required	Hidden
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

Registration options

Define the registration tools to be used in the pipeline.

Parameter	Description	Type	Default	Required	Hidden
run_easyreg	Run freesurfer EasyReg any-to-any modality registration. Help Needs freesurfer license.	boolean	False
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	False

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
tractometry_covariates	Comma separated list of covariates to include in the tractometry analysis. Help Comma separated list of covariates to include in the tractometry analysis.	string	site,age,sex,handedness,disease

Reconst FW NODDI options

Define the behaviour of the reconst_fw_noddi subworkflow.

Parameter	Description	Type	Default	Required	Hidden
run_noddi	Compute NODDI maps. Help Compute NODDI maps.	boolean	False
run_freewater	Run Freewater Elimination and compute Freewater corrected metrics. Help Run Freewater Elimination and compute Freewater corrected metrics.	boolean	False
average_diff_priors	Average diffusivity priors across subjects. Help Average diffusivity priors across subjects.	boolean
para_diff	Average parallel diffusivity value (mm²/s). Help Average parallel diffusivity value. Specifying this will override automatically computed values.	number	0.0015
iso_diff	Average isotropic diffusivity value (mm²/s). Help Average isotropic diffusivity value. Specifying this will override automatically computed values.	number	0.003
perp_diff_min	Minimum perpendicular diffusivity value (mm²/s). Help Minimum perpendicular diffusivity value. Specifying this will override automatically computed values.	number	0.0001
perp_diff_max	Maximum perpendicular diffusivity value (mm²/s). Help Maximum perpendicular diffusivity value. Specifying this will override automatically computed values.	number	0.0007
noddi_lambda1	NODDI first regularization parameter.	number	0.5
noddi_lambda2	NODDI second regularization parameter.	number	0.001
fw_lambda1	Freeewater first regularization parameter.	number	0.0
fw_lambda2	Freewater second regularization parameter.	number	0.25

Atlas-based ROI metrics options

Define the behaviour of the atlas_roimetrics subworkflow.

Parameter	Description	Type	Default	Required	Hidden
run_atlas_roimetrics	Run atlas-based ROI metrics. The atlas used must be specified using one of the ‘use_atlas_’ parameters. Help Run atlas-based ROI metrics. The atlas used must be specified using one of the ‘use_atlas_’ parameters.	boolean	False

Atlas IIT options

Define the behaviour of the atlas_iit subworkflow.

Parameter	Description	Type	Default	Required	Hidden
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
use_atlas_iit	Use the IIT atlas for atlas-based ROI metrics. Help Use the IIT atlas for atlas-based ROI metrics.	boolean	True
use_binary_masks	If ‘true’, the IIT bundle masks will be thresholded to create binary masks before extracting the metrics. Help IIT bundle masks will be thresholded to create binary masks before extracting the metrics.	boolean	False

Harmonization options

Parameters to configure the harmonization subworkflow.

Parameter	Description	Type	Default	Required	Hidden
harmonization_reference	TSV file of the reference site used to harmonize the current site (e.g. the output TSV from stats/metrics in roi). Help TSV file of the reference site used to harmonize the current site (e.g. the output TSV from stats/metrics in roi).	string

Output to different spaces options

Options for outputting to specific spaces.

Parameter	Description	Type	Default	Required	Hidden
output_orig_space	If set, the results will be outputted in the T1 orig space. Help Images, masks, labels will be outputted in the T1 orig space.	boolean	False
output_template_space	If set, the results will be outputted in the specified template space using TemplateFlow. Help Please see their documentation for an exhaustive list (https://www.templateflow.org/browse/)	boolean	False
template	Template space to output to. The available template are the ones supported by TemplateFlow. Help Please see their documentation for an exhaustive list (https://www.templateflow.org/browse/)	string	None		False
templateflow_resolution	Resolution of the template space. Help Typically 1 or 2 (mm).	integer			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). Help Please see their documentation for an exhaustive list (https://www.templateflow.org/browse/)	integer			False
templateflow_home	Path to the TemplateFlow home directory where templates will be downloaded. Help If you are running the pipeline without internet access, this needs to point to a folder containing predownloaded templates.	string	./templateflow		False

Other parameters

Parameter	Description	Type	Default	Required	Hidden
hook_url	Hook URL to notify a web server e.g. Microsoft Teams and Slack Help Hook URL to notify a web server e.g. Microsoft Teams and Slack	string
use_template_t2w	Use the T2w template from TemplateFlow for registration. Help Use the T2w template from TemplateFlow for registration.	boolean
match_t1_run	If there’s multiple T1w images for a single single DWI run, this option will try to match the T1w and DWI runs based on their run number. Help If there’s multiple T1w images for a single single DWI run, this option will try to match the T1w and DWI runs based on their run number.	boolean	True
noddi_ignore_single_shell	If enabled, the subjects with single shell DWI acquisitions will be ignored in the NODDI fitting and will not fail the pipeline. Help If enabled, the subjects with single shell DWI acquisitions will be ignored in the NODDI fitting and will not fail the pipeline.	boolean