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nextflow_schema.json
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nextflow_schema.json
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{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/nf/pediatric/master/nextflow_schema.json",
"title": "nf/pediatric pipeline parameters",
"description": "nf-pediatric is a neuroimaging pipeline to process pediatric MRI data (including fMRI, dMRI, and sMRI) ranging from 0-18 years old.",
"type": "object",
"$defs": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"schema": "assets/schema_input.json",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.",
"fa_icon": "fas fa-file-csv"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "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.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
},
"multiqc_title": {
"type": "string",
"description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
"fa_icon": "fas fa-file-signature"
}
}
},
"freesurfer_options": {
"title": "FreeSurfer/FastSurfer Options",
"type": "object",
"fa_icon": "fas fa-brain",
"description": "Options for FreeSurfer and FastSurfer processing.",
"help_text": "These options are used to configure the FreeSurfer and FastSurfer processing steps in the pipeline. You can use these options to customise the behaviour of the FreeSurfer and FastSurfer steps.",
"properties": {
"use_fastsurfer": {
"type": "boolean",
"description": "Use FastSurfer instead of FreeSurfer.",
"fa_icon": "fas fa-rocket",
"default": false,
"hidden": false
},
"fs_license": {
"type": "string",
"description": "Path to FreeSurfer license file.",
"fa_icon": "fas fa-file-signature",
"help_text": "Path to FreeSurfer license file. This is required to run FreeSurfer. You can obtain a FreeSurfer license from the FreeSurfer website.",
"format": "file-path",
"exists": true
},
"acq3T": {
"type": "boolean",
"description": "Use 3T acquisition parameters.",
"fa_icon": "fas fa-magnet",
"default": true,
"hidden": true
}
}
},
"atlases_options": {
"title": "Atlases Options",
"type": "object",
"fa_icon": "fas fa-map-marked-alt",
"description": "Options for atlases used in the pipeline.",
"help_text": "These options are used to configure the atlases used in the pipeline. You can use these options to customise the behaviour of the atlases.",
"properties": {
"utils_folder": {
"type": "string",
"description": "Path to the utils folder.",
"fa_icon": "fas fa-folder",
"help_text": "Path to the utils folder. This folder contains the atlases used in the pipeline. You can download the utils folder from the nf-pediatric GitHub repository.",
"format": "directory-path",
"exists": true,
"hidden": true
}
}
},
"t1_processing_options": {
"title": "T1 Processing Options",
"type": "object",
"fa_icon": "fas fa-brain",
"description": "Options for T1 processing.",
"help_text": "These options are used to configure the T1 processing steps in the pipeline. You can use these options to customise the behaviour of the T1 processing steps.",
"properties": {
"t1_denoise_number_of_coils": {
"type": "integer",
"description": "Number of coils used in the T1 denoising step.",
"fa_icon": "fas fa-brain",
"default": 1,
"hidden": true
},
"t1_bias_bspline_knot_per_voxel": {
"type": "number",
"description": "Number of B-spline knots per voxel used in the T1 bias correction step.",
"fa_icon": "fas fa-brain",
"default": 1,
"hidden": true
},
"t1_bias_shrink_factor": {
"type": "integer",
"description": "Shrink factor used in the T1 bias correction step.",
"fa_icon": "fas fa-brain",
"default": 1,
"hidden": true
},
"t1_resample_voxel_size": {
"type": "integer",
"description": "Voxel size used in the T1 resampling step.",
"fa_icon": "fas fa-brain",
"default": 1,
"hidden": true
},
"t1_resample_interp": {
"type": "string",
"description": "Interpolation method used in the T1 resampling step.",
"fa_icon": "fas fa-brain",
"default": "lin",
"hidden": true
},
"t1_run_synthstrip": {
"type": "boolean",
"description": "Run SynthStrip for brain extraction rather than AntsBet.",
"fa_icon": "fas fa-brain",
"default": false,
"hidden": false
},
"t1_synthstrip_border": {
"type": "integer",
"description": "Border used in the SynthStrip brain extraction step.",
"fa_icon": "fas fa-brain",
"default": 1,
"hidden": true
},
"t1_synthstrip_nocsf": {
"type": "boolean",
"description": "Do not use CSF in the SynthStrip brain extraction step.",
"fa_icon": "fas fa-brain",
"default": false,
"hidden": true
},
"t1_synthstrip_weights": {
"type": "string",
"description": "Alternative weights used in the SynthStrip brain extraction step.",
"fa_icon": "fas fa-brain",
"default": null,
"hidden": false
},
"t1_bet_template": {
"type": "string",
"description": "Path to the template to use in antsBet",
"fa_icon": "fas fa-brain",
"hidden": true
},
"t1_bet_template_probability_map": {
"type": "string",
"description": "Path to the template probability map to use in antsBet",
"fa_icon": "fas fa-brain",
"hidden": true
}
}
},
"dwi_preprocessing_options": {
"title": "DWI Preprocessing Options",
"type": "object",
"fa_icon": "fas fa-brain",
"description": "Options for DWI preprocessing.",
"help_text": "These options are used to configure the DWI preprocessing steps in the pipeline. You can use these options to customise the behaviour of the DWI preprocessing steps.",
"properties": {
"dwi_denoise_patch_size": {
"type": "integer",
"description": "Patch size used in the DWI denoising step.",
"fa_icon": "fas fa-brain",
"default": 7,
"hidden": true
},
"dwi_susceptibility_config_file": {
"type": "string",
"description": "Path to the susceptibility distortion correction config file.",
"fa_icon": "fas fa-brain",
"default": "b02b0.cnf",
"hidden": true
},
"dwi_susceptibility_output_prefix": {
"type": "string",
"description": "Prefix used in the susceptibility distortion correction step.",
"fa_icon": "fas fa-brain",
"default": "topup_results",
"hidden": true
},
"dwi_susceptibility_readout": {
"type": "number",
"description": "Readout time used in the susceptibility distortion correction step.",
"fa_icon": "fas fa-brain",
"default": 0.04,
"hidden": true
},
"dwi_susceptibility_b0_threshold": {
"type": "integer",
"description": "B0 threshold used in the susceptibility distortion correction step.",
"fa_icon": "fas fa-brain",
"default": 20,
"hidden": true
},
"dwi_susceptibility_encoding_dir": {
"type": "string",
"description": "Encoding direction used in the susceptibility distortion correction step.",
"fa_icon": "fas fa-brain",
"default": "y",
"hidden": true
},
"dwi_motion_and_eddy_command": {
"type": "string",
"description": "Command used in the motion and eddy correction step.",
"fa_icon": "fas fa-brain",
"default": "eddy_cpu",
"hidden": true
},
"dwi_motion_and_eddy_bet_f_threshold": {
"type": "number",
"description": "Bet f threshold used in the motion and eddy correction step.",
"fa_icon": "fas fa-brain",
"default": 0.16,
"hidden": true
},
"dwi_motion_and_eddy_restore_slices": {
"type": "boolean",
"description": "Restore slices in the motion and eddy correction step.",
"fa_icon": "fas fa-brain",
"default": true,
"hidden": true
},
"dwi_pwdavg_shells": {
"type": "string",
"description": "Shells used in the PowderAverage step.",
"fa_icon": "fas fa-brain",
"hidden": false
},
"dwi_pwdavg_shell_thr": {
"type": "integer",
"description": "Shell threshold used in the PowderAverage step.",
"fa_icon": "fas fa-brain",
"default": 50,
"hidden": true
},
"dwi_pwdavg_b0_thr": {
"type": "integer",
"description": "B0 threshold used in the PowderAverage step.",
"fa_icon": "fas fa-brain",
"default": 20,
"hidden": true
},
"dwi_run_synthstrip": {
"type": "boolean",
"description": "Run SynthStrip for brain extraction",
"fa_icon": "fas fa-brain",
"default": false,
"hidden": false
},
"dwi_synthstrip_border": {
"type": "integer",
"description": "Border used in the SynthStrip brain extraction step.",
"fa_icon": "fas fa-brain",
"default": 1,
"hidden": true
},
"dwi_synthstrip_nocsf": {
"type": "boolean",
"description": "Do not use CSF in the SynthStrip brain extraction step.",
"fa_icon": "fas fa-brain",
"default": false,
"hidden": true
},
"dwi_synthstrip_weights": {
"type": "string",
"description": "Alternative weights used in the SynthStrip brain extraction step.",
"fa_icon": "fas fa-brain",
"default": null,
"hidden": false
},
"dwi_bet_f_threshold": {
"type": "number",
"description": "Bet f threshold used in the brain extraction step.",
"fa_icon": "fas fa-brain",
"default": 0.16,
"hidden": true
},
"dwi_bet_b0_threshold": {
"type": "integer",
"description": "B0 threshold used in the brain extraction step.",
"fa_icon": "fas fa-brain",
"default": 20,
"hidden": true
},
"dwi_bias_bspline_knot_per_voxel": {
"type": "number",
"description": "Number of B-spline knots per voxel used in the DWI bias correction step.",
"fa_icon": "fas fa-brain",
"default": 0.25,
"hidden": true
},
"dwi_bias_shrink_factor": {
"type": "integer",
"description": "Shrink factor used in the DWI bias correction step.",
"fa_icon": "fas fa-brain",
"default": 4,
"hidden": true
},
"dwi_normalize_fa_mask_threshold": {
"type": "number",
"description": "FA mask threshold used in the normalization step.",
"fa_icon": "fas fa-brain",
"default": 0.4,
"hidden": false
},
"dwi_normalize_shell_tolerance": {
"type": "integer",
"description": "Shell tolerance used in the normalization step.",
"fa_icon": "fas fa-brain",
"default": 50,
"hidden": true
},
"dwi_resample_voxel_size": {
"type": "integer",
"description": "Voxel size used in the DWI resampling step.",
"fa_icon": "fas fa-brain",
"default": 1,
"hidden": true
},
"dwi_resample_interp": {
"type": "string",
"description": "Interpolation method used in the DWI resampling step.",
"fa_icon": "fas fa-brain",
"default": "lin",
"hidden": true
},
"dwi_resample_mask_voxel_size": {
"type": "integer",
"description": "Voxel size used in the DWI mask resampling step.",
"fa_icon": "fas fa-brain",
"default": 1,
"hidden": true
},
"dwi_resample_mask_interp": {
"type": "string",
"description": "Interpolation method used in the DWI mask resampling step.",
"fa_icon": "fas fa-brain",
"default": "nn",
"hidden": true
},
"dwi_extract_b0_threshold": {
"type": "integer",
"description": "B0 threshold used in the DWI extraction step.",
"fa_icon": "fas fa-brain",
"default": 20,
"hidden": true
}
}
},
"dti_options": {
"title": "DTI Options",
"type": "object",
"fa_icon": "fas fa-brain",
"description": "Options for DTI processing.",
"help_text": "These options are used to configure the DTI processing steps in the pipeline. You can use these options to customise the behaviour of the DTI processing steps.",
"properties": {
"dti_shell_tolerance": {
"type": "integer",
"description": "Shell tolerance used in the DTI processing step.",
"fa_icon": "fas fa-brain",
"default": 50,
"hidden": true
},
"dti_max_shell_value": {
"type": "integer",
"description": "Maximum shell value used in the DTI processing step.",
"fa_icon": "fas fa-brain",
"default": 1500,
"hidden": false
},
"dti_b0_threshold": {
"type": "integer",
"description": "B0 threshold used in the DTI processing step.",
"fa_icon": "fas fa-brain",
"default": 20,
"hidden": true
}
}
},
"frf_options": {
"title": "FRF Options",
"type": "object",
"fa_icon": "fas fa-brain",
"description": "Options for FRF processing.",
"help_text": "These options are used to configure the FRF processing steps in the pipeline. You can use these options to customise the behaviour of the FRF processing steps.",
"properties": {
"frf_fa": {
"type": "number",
"description": "Minimum FA threshold to use to compute the FRF.",
"fa_icon": "fas fa-brain",
"default": 0.7,
"hidden": true
},
"frf_min_fa": {
"type": "number",
"description": "Minimum FA threshold to use to compute the FRF.",
"fa_icon": "fas fa-brain",
"default": 0.5,
"hidden": true
},
"frf_nvox_min": {
"type": "integer",
"description": "Minimum number of voxels to include in the computation of the FRF.",
"fa_icon": "fas fa-brain",
"default": 300,
"hidden": true
},
"frf_roi_radius": {
"type": "integer",
"description": "Radius of the ROI used to compute the FRF.",
"fa_icon": "fas fa-brain",
"default": 20,
"hidden": true
},
"frf_dwi_shell_tolerance": {
"type": "integer",
"description": "Shell tolerance used in the DWI processing step.",
"fa_icon": "fas fa-brain",
"default": 50,
"hidden": true
},
"frf_max_dti_shell_value": {
"type": "integer",
"description": "Maximum DTI shell value used.",
"fa_icon": "fas fa-brain",
"default": 1500,
"hidden": false
},
"frf_min_fodf_shell_value": {
"type": "integer",
"description": "Minimum FODF shell value used.",
"fa_icon": "fas fa-brain",
"default": 100,
"hidden": false
},
"frf_b0_threshold": {
"type": "integer",
"description": "B0 threshold used in the FRF processing step.",
"fa_icon": "fas fa-brain",
"default": 20,
"hidden": true
},
"frf_set_method": {
"type": "string",
"description": "Method used to compute the FRF.",
"fa_icon": "fas fa-brain",
"default": "ssst",
"choices": ["ssst", "msmt"],
"hidden": false
},
"frf_set_frf": {
"type": "boolean",
"description": "Use a manually set FRF.",
"fa_icon": "fas fa-brain",
"default": true,
"hidden": false
},
"frf_manual_frf": {
"type": "string",
"description": "Manual FRF values.",
"fa_icon": "fas fa-brain",
"default": "15,4,4",
"hidden": false
},
"frf_mean_frf": {
"type": "boolean",
"description": "Use the mean FRF across subjects.",
"fa_icon": "fas fa-brain",
"default": false,
"hidden": false
}
}
},
"fodf_options": {
"title": "FODF Options",
"type": "object",
"fa_icon": "fas fa-brain",
"description": "Options for FODF processing.",
"help_text": "These options are used to configure the FODF processing steps in the pipeline. You can use these options to customise the behaviour of the FODF processing steps.",
"properties": {
"fodf_shell_tolerance": {
"type": "integer",
"description": "Shell tolerance used in the FODF processing step.",
"fa_icon": "fas fa-brain",
"default": 50,
"hidden": true
},
"fodf_min_fodf_shell_value": {
"type": "integer",
"description": "Minimum FODF shell value used.",
"fa_icon": "fas fa-brain",
"default": 100,
"hidden": false
},
"fodf_b0_threshold": {
"type": "integer",
"description": "B0 threshold used in the FODF processing step.",
"fa_icon": "fas fa-brain",
"default": 20,
"hidden": true
},
"fodf_sh_order": {
"type": "integer",
"description": "Spherical harmonics order used in the FODF processing step.",
"fa_icon": "fas fa-brain",
"default": 8,
"hidden": false
},
"fodf_sh_basis": {
"type": "string",
"description": "Spherical harmonics basis used in the FODF processing step.",
"fa_icon": "fas fa-brain",
"default": "descoteaux07",
"choices": ["descoteaux07", "tournier07"],
"hidden": false
},
"fodf_set_method": {
"type": "string",
"description": "Method used to compute the FODF.",
"fa_icon": "fas fa-brain",
"default": "ssst",
"choices": ["ssst", "msmt"],
"hidden": false
},
"fodf_relative_threshold": {
"type": "number",
"description": "Relative threshold used in the FODF processing step.",
"fa_icon": "fas fa-brain",
"default": 0.1,
"hidden": true
},
"fodf_a_factor": {
"type": "number",
"description": "FODF a factor used in the FODF processing step.",
"fa_icon": "fas fa-brain",
"default": 2.0,
"hidden": true
},
"fodf_max_fa_threshold": {
"type": "number",
"description": "Maximum FA threshold used in the FODF processing step.",
"fa_icon": "fas fa-brain",
"default": 0.1,
"hidden": true
},
"fodf_min_md_threshold": {
"type": "number",
"description": "Minimum MD threshold used in the FODF processing step.",
"fa_icon": "fas fa-brain",
"default": 0.003,
"hidden": true
}
}
},
"registration_options": {
"title": "Registration Options",
"type": "object",
"fa_icon": "fas fa-brain",
"description": "Options for registration.",
"help_text": "These options are used to configure the registration steps in the pipeline. You can use these options to customise the behaviour of the registration steps.",
"properties": {
"reg_dimensionality": {
"type": "integer",
"description": "Dimensionality of the registered image.",
"fa_icon": "fas fa-brain",
"default": 3,
"hidden": true
},
"reg_interpolation": {
"type": "string",
"description": "Interpolation method used in the registration step.",
"fa_icon": "fas fa-brain",
"default": "NearestNeighbor",
"choices": ["NearestNeighbor", "Linear", "BSpline"],
"hidden": true
},
"reg_output_dtype": {
"type": "string",
"description": "Output data type used in the registration step.",
"fa_icon": "fas fa-brain",
"default": "int",
"choices": ["float", "int"],
"hidden": true
}
}
},
"pft_tracking_options": {
"title": "PFT Tracking Options",
"type": "object",
"fa_icon": "fas fa-brain",
"description": "Options for PFT tracking.",
"help_text": "These options are used to configure the PFT tracking steps in the pipeline. You can use these options to customise the behaviour of the PFT tracking steps.",
"properties": {
"run_pft_tracking": {
"type": "boolean",
"description": "Run PFT tracking.",
"fa_icon": "fas fa-brain",
"default": true,
"hidden": false
},
"pft_fa_threshold": {
"type": "number",
"description": "FA threshold used in the PFT tracking step.",
"fa_icon": "fas fa-brain",
"default": 0.2,
"hidden": true
},
"pft_seeding_mask_type": {
"type": "string",
"description": "Seeding mask type used in the PFT tracking step.",
"fa_icon": "fas fa-brain",
"default": "wm",
"choices": ["wm", "fa", "interface"],
"hidden": false
},
"pft_random_seed": {
"type": "integer",
"description": "Random seed used in the PFT tracking step.",
"fa_icon": "fas fa-brain",
"default": 1234,
"hidden": true
},
"pft_compress": {
"type": "boolean",
"description": "If true, compress the streamlines.",
"fa_icon": "fas fa-brain",
"default": true,
"hidden": true
},
"pft_compress_value": {
"type": "number",
"description": "Compression value for the streamlines' compression.",
"fa_icon": "fas fa-brain",
"default": 0.2,
"hidden": true
},
"pft_algo": {
"type": "string",
"description": "Algorithm used in the PFT tracking step.",
"fa_icon": "fas fa-brain",
"default": "prob",
"choices": ["prob", "det"],
"hidden": false
},
"pft_nbr_seeds": {
"type": "integer",
"description": "Number of seeds used in the PFT tracking step.",
"fa_icon": "fas fa-brain",
"default": 10,
"hidden": false
},
"pft_seeding_type": {
"type": "string",
"description": "Seeding type used in the PFT tracking step.",
"fa_icon": "fas fa-brain",
"default": "npv",
"choices": ["npv", "nt"],
"hidden": false
},
"pft_step": {
"type": "number",
"description": "Step value used in the PFT tracking step.",
"fa_icon": "fas fa-brain",
"default": 0.5,
"hidden": true
},
"pft_theta": {
"type": "number",
"description": "Theta value used in the PFT tracking step.",
"fa_icon": "fas fa-brain",
"default": 20,
"hidden": true
},
"pft_sfthres": {
"type": "number",
"description": "SF threshold used in the PFT tracking step.",
"fa_icon": "fas fa-brain",
"default": 0.1,
"hidden": true
},
"pft_sfthres_init": {
"type": "number",
"description": "Initial SF threshold used in the PFT tracking step.",
"fa_icon": "fas fa-brain",
"default": 0.5,
"hidden": true
},
"pft_min_len": {
"type": "number",
"description": "Minimum length used in the PFT tracking step.",
"fa_icon": "fas fa-brain",
"default": 20,
"hidden": false
},
"pft_max_len": {
"type": "number",
"description": "Maximum length used in the PFT tracking step.",
"fa_icon": "fas fa-brain",
"default": 200,
"hidden": false
},
"pft_particles": {
"type": "integer",
"description": "Number of particles used in the PFT tracking step.",
"fa_icon": "fas fa-brain",
"default": 15,
"hidden": true
},
"pft_back": {
"type": "integer",
"description": "Back value used in the PFT tracking step.",
"fa_icon": "fas fa-brain",
"default": 2,
"hidden": true
},
"pft_front": {
"type": "integer",
"description": "Front value used in the PFT tracking step.",
"fa_icon": "fas fa-brain",
"default": 1,
"hidden": true
},
"pft_sh_basis": {
"type": "string",
"description": "Spherical harmonics basis used in the PFT tracking step.",
"fa_icon": "fas fa-brain",
"default": "descoteaux07",
"choices": ["descoteaux07", "tournier07"],
"hidden": false
}
}
},
"local_tracking_options": {
"title": "Local Tracking Options",
"type": "object",
"fa_icon": "fas fa-brain",
"description": "Options for local tracking.",
"help_text": "These options are used to configure the local tracking steps in the pipeline. You can use these options to customise the behaviour of the local tracking steps.",
"properties": {
"run_local_tracking": {
"type": "boolean",
"description": "Run local tracking.",
"fa_icon": "fas fa-brain",
"default": true,
"hidden": false
},
"local_fa_tracking_mask_threshold": {
"type": "number",
"description": "FA threshold used for the tracking mask.",
"fa_icon": "fas fa-brain",
"default": 0.4,
"hidden": true
},
"local_fa_seeding_mask_threshold": {
"type": "number",
"description": "FA threshold used for the seeding mask.",
"fa_icon": "fas fa-brain",
"default": 0.4,
"hidden": true
},
"local_seeding_mask_type": {
"type": "string",
"description": "Seeding mask type used in the local tracking step.",
"fa_icon": "fas fa-brain",
"default": "wm",
"choices": ["wm", "fa", "interface"],
"hidden": false
},
"local_tracking_mask_type": {
"type": "string",
"description": "Tracking mask type used in the local tracking step.",
"fa_icon": "fas fa-brain",
"default": "wm",
"choices": ["wm", "fa", "interface"],
"hidden": false
},
"local_random_seed": {
"type": "integer",
"description": "Random seed used in the local tracking step.",
"fa_icon": "fas fa-brain",
"default": 1234,
"hidden": true
},
"local_compress": {
"type": "boolean",
"description": "If true, compress the streamlines.",
"fa_icon": "fas fa-brain",
"default": true,
"hidden": true
},
"local_compress_value": {
"type": "number",
"description": "Compression value for the streamlines' compression.",
"fa_icon": "fas fa-brain",
"default": 0.2,
"hidden": true
},
"local_algo": {
"type": "string",
"description": "Algorithm used in the local tracking step.",
"fa_icon": "fas fa-brain",
"default": "prob",
"choices": ["prob", "det"],
"hidden": false
},
"local_nbr_seeds": {
"type": "integer",
"description": "Number of seeds used in the local tracking step.",
"fa_icon": "fas fa-brain",
"default": 10,
"hidden": false
},
"local_seeding_type": {
"type": "string",
"description": "Seeding type used in the local tracking step.",
"fa_icon": "fas fa-brain",
"default": "npv",
"choices": ["npv", "nt"],
"hidden": false
},
"local_step": {
"type": "number",
"description": "Step value used in the local tracking step.",
"fa_icon": "fas fa-brain",
"default": 0.5,
"hidden": true
},
"local_theta": {
"type": "number",
"description": "Theta value used in the local tracking step.",
"fa_icon": "fas fa-brain",
"default": 20,
"hidden": true
},
"local_sfthres": {
"type": "number",
"description": "SF threshold used in the local tracking step.",
"fa_icon": "fas fa-brain",
"default": 0.1,
"hidden": true
},
"local_min_len": {
"type": "number",
"description": "Minimum length used in the local tracking step.",
"fa_icon": "fas fa-brain",
"default": 20,
"hidden": false
},
"local_max_len": {
"type": "number",
"description": "Maximum length used in the local tracking step.",
"fa_icon": "fas fa-brain",
"default": 200,
"hidden": false
},
"local_sh_basis": {
"type": "string",
"description": "Spherical harmonics basis used in the local tracking step.",
"fa_icon": "fas fa-brain",
"default": "descoteaux07",
"choices": ["descoteaux07", "tournier07"],
"hidden": false
}
}
},
"transform_labels_options": {
"title": "Transform Labels Options",
"type": "object",
"fa_icon": "fas fa-brain",
"description": "Options for transforming labels.",
"help_text": "These options are used to configure the transformation of labels in the pipeline. You can use these options to customise the behaviour of the label transformation steps.",
"properties": {
"labels_transform_dimensionality": {
"type": "integer",
"description": "Dimensionality of the label file.",
"fa_icon": "fas fa-brain",
"default": 3,
"hidden": false
},
"labels_output_suffix": {
"type": "string",
"description": "Name to use as suffix in the output filename.",
"fa_icon": "fas fa-brain",
"default": "_labels",
"hidden": true
},
"labels_interpolation": {
"type": "string",
"description": "Interpolation method used in the label transformation step.",
"fa_icon": "fas fa-brain",
"default": "NearestNeighbor",
"choices": ["NearestNeighbor", "Linear", "BSpline"],
"hidden": true
},
"labels_output_dtype": {
"type": "string",
"description": "Output data type used in the label transformation step.",
"fa_icon": "fas fa-brain",
"default": "int",
"choices": ["float", "int"],
"hidden": true
}
}
},
"commit_options": {
"title": "COMMIT Options",
"type": "object",
"fa_icon": "fas fa-code-branch",
"description": "Options for COMMIT filtering.",
"help_text": "These options are used to configure the COMMIT filtering steps in the pipeline. You can use these options to customise the behaviour of the COMMIT filtering steps.",
"properties": {
"run_commit2": {
"type": "boolean",
"description": "Run COMMIT2 filtering.",
"fa_icon": "fas fa-code-branch",
"default": true,
"hidden": false
},
"commit2_lambda": {
"type": "number",
"description": "Lambda value used in the COMMIT filtering step.",
"fa_icon": "fas fa-code-branch",
"default": 0.001,
"hidden": true
},
"commit_para_diff": {
"type": "string",
"description": "Para diff value used in the COMMIT filtering step.",
"fa_icon": "fas fa-code-branch",
"hidden": false
},
"commit_iso_diff": {
"type": "string",
"description": "Iso diff value used in the COMMIT filtering step.",
"fa_icon": "fas fa-code-branch",
"hidden": false
},
"commit_perp_diff": {
"type": "string",
"description": "Perp diff value used in the COMMIT filtering step.",
"fa_icon": "fas fa-code-branch",
"hidden": false
},
"commit_ball_stick": {
"type": "boolean",
"description": "Use the ball and stick model in the COMMIT filtering step.",
"fa_icon": "fas fa-code-branch",
"default": false,
"hidden": true
},
"commit_nbr_dir": {
"type": "integer",
"description": "Number of directions used in the COMMIT filtering step.",
"fa_icon": "fas fa-code-branch",
"default": 500,
"hidden": true
},
"commit_shell_tolerance": {
"type": "integer",
"description": "Shell tolerance used in the COMMIT filtering step.",
"fa_icon": "fas fa-code-branch",
"default": 20,
"hidden": true
}
}
},
"decompose_options": {
"title": "Decompose Tractogram Options",
"type": "object",
"fa_icon": "fas fa-brain",
"description": "Options for decomposing the tractogram.",
"help_text": "These options are used to configure the decomposition of the tractogram in the pipeline. You can use these options to customise the behaviour of the tractogram decomposition steps.",
"properties": {
"decompose_no_pruning": {