%YAML 1.1
---
# CPAC Pipeline Configuration YAML file
# Version 1.8.8.dev1
#
# http://fcp-indi.github.io for more info.
#
# Tip: This file can be edited manually with a text editor for quick modifications.
FROM: fmriprep-options
pipeline_setup:
# Name for this pipeline configuration - useful for identification.
# This string will be sanitized and used in filepaths
pipeline_name: RBCv0
output_directory:
# Quality control outputs
quality_control:
# Generate eXtensible Connectivity Pipeline-style quality control files
generate_xcpqc_files: On
system_config:
# Stop worklow execution on first crash?
fail_fast: On
# Random seed used to fix the state of execution.
# If unset, each process uses its own default.
# If set, a `random.log` file will be generated logging the random seed and each node to which that seed was applied.
# If set to a positive integer (up to 2147483647), that integer will be used to seed each process that accepts a random seed.
# If set to 'random', a random positive integer (up to 2147483647) will be generated and that seed will be used to seed each process that accepts a random seed.
random_seed: 77742777
registration_workflows:
anatomical_registration:
# Template to be used during registration.
# It is not necessary to change this path unless you intend to use a non-standard template.
T1w_brain_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz
# Template to be used during registration.
# It is not necessary to change this path unless you intend to use a non-standard template.
T1w_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
# Template to be used during registration.
# It is not necessary to change this path unless you intend to use a non-standard template.
T1w_brain_template_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
functional_registration:
func_registration_to_template:
output_resolution:
# The resolution (in mm) to which the preprocessed, registered functional timeseries outputs are written into.
# NOTE:
# selecting a 1 mm or 2 mm resolution might substantially increase your RAM needs- these resolutions should be selected with caution.
# for most cases, 3 mm or 4 mm resolutions are suggested.
# NOTE:
# this also includes the single-volume 3D preprocessed functional data,
# such as the mean functional (mean EPI) in template space
func_preproc_outputs: 2mm
# The resolution (in mm) to which the registered derivative outputs are written into.
# NOTE:
# this is for the single-volume functional-space outputs (i.e. derivatives)
# thus, a higher resolution may not result in a large increase in RAM needs as above
func_derivative_outputs: 2mm
target_template:
T1_template:
# Standard Skull Stripped Template. Used as a reference image for functional registration.
# This can be different than the template used as the reference/fixed for T1-to-template registration.
T1w_brain_template_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
# Standard Anatomical Brain Image with Skull.
# This can be different than the template used as the reference/fixed for T1-to-template registration.
T1w_template_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}.nii.gz
# Template to be used during registration.
# It is not necessary to change this path unless you intend to use a non-standard template.
T1w_brain_template_mask_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain_mask.nii.gz
# a standard template for resampling if using float resolution
T1w_template_for_resample: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
functional_preproc:
distortion_correction:
# using: ['PhaseDiff', 'Blip', 'Blip-FSL-TOPUP']
# PhaseDiff - Perform field map correction using a single phase difference image, a subtraction of the two phase images from each echo. Default scanner for this method is SIEMENS.
# Blip - Uses AFNI 3dQWarp to calculate the distortion unwarp for EPI field maps of opposite/same phase encoding direction.
# Blip-FSL-TOPUP - Uses FSL TOPUP to calculate the distortion unwarp for EPI field maps of opposite/same phase encoding direction.
using: [PhaseDiff, Blip-FSL-TOPUP]
func_masking:
FSL_AFNI:
brain_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
brain_probseg: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
truncation:
# First timepoint to include in analysis.
# Default is 0 (beginning of timeseries).
# First timepoint selection in the scan parameters in the data configuration file, if present, will over-ride this selection.
# Note: the selection here applies to all scans of all participants.
start_tr: 2
despiking:
# Run AFNI 3dDespike
# this is a fork point
# run: [On, Off] - this will run both and fork the pipeline
run: [On]
space: template
nuisance_corrections:
2-nuisance_regression:
# this is a fork point
# run: [On, Off] - this will run both and fork the pipeline
run: [On]
# Select which nuisance signal corrections to apply
Regressors:
- Name: 36_parameter
Bandpass:
bottom_frequency: 0.01
top_frequency: 0.1
CerebrospinalFluid:
erode_mask: Off
extraction_resolution: 2
include_delayed: On
include_delayed_squared: On
include_squared: On
summary: Mean
GlobalSignal:
include_delayed: On
include_delayed_squared: On
include_squared: On
summary: Mean
Motion:
include_delayed: On
include_delayed_squared: On
include_squared: On
WhiteMatter:
erode_mask: Off
extraction_resolution: 2
include_delayed: On
include_delayed_squared: On
include_squared: On
summary: Mean
- Name: aCompCor
Bandpass:
bottom_frequency: 0.01
top_frequency: 0.1
CerebrospinalFluid:
erode_mask: Off
extraction_resolution: 2
include_delayed: On
include_delayed_squared: On
include_squared: On
summary: Mean
aCompCor:
summary:
method: DetrendPC
components: 5
tissues:
- WhiteMatter
- CerebrospinalFluid
extraction_resolution: 2
Motion:
include_delayed: On
include_delayed_squared: On
include_squared: On
WhiteMatter:
erode_mask: Off
extraction_resolution: 2
include_delayed: On
include_delayed_squared: On
include_squared: On
summary: Mean
# Process and refine masks used to produce regressors and time series for
# regression.
regressor_masks:
erode_csf:
# Erode cerebrospinal fluid mask in millimeters, default for cerebrospinal fluid is 30mm
# Cerebrospinal fluid erosion default is using millimeters.
csf_mask_erosion_mm:
# Target volume ratio, if using erosion.
# Default proportion is None for cerebrospinal fluid mask.
# If using erosion, using both proportion and millimeters is not recommended.
csf_erosion_prop: 0.9
timeseries_extraction:
run: On
connectivity_matrix:
# Create a connectivity matrix from timeseries data
# Options:
# ['AFNI', 'Nilearn', 'ndmg']
using: [Nilearn]
# Enter paths to region-of-interest (ROI) NIFTI files (.nii or .nii.gz) to be used for time-series extraction, and then select which types of analyses to run.
# Denote which analyses to run for each ROI path by listing the names below. For example, if you wish to run Avg and SpatialReg, you would enter: '/path/to/ROI.nii.gz': Avg, SpatialReg
# available analyses:
# /path/to/atlas.nii.gz: Avg, Voxel, SpatialReg
tse_roi_paths:
/ndmg_atlases/label/Human/AAL_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
/ndmg_atlases/label/Human/Brodmann_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
/ndmg_atlases/label/Human/Glasser_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
/ndmg_atlases/label/Human/Slab907_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
/ndmg_atlases/label/Human/HarvardOxfordcort-maxprob-thr25_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
/ndmg_atlases/label/Human/HarvardOxfordsub-maxprob-thr25_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
/ndmg_atlases/label/Human/Juelich_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
/cpac_templates/CC200.nii.gz: Avg
/cpac_templates/CC400.nii.gz: Avg
/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-200Parcels17NetworksOrder.nii.gz: Avg
/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-300Parcels17NetworksOrder.nii.gz: Avg
/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-400Parcels17NetworksOrder.nii.gz: Avg
/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-1000Parcels17NetworksOrder.nii.gz: Avg
/ndmg_atlases/label/Human/Yeo-17-liberal_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
/ndmg_atlases/label/Human/Yeo-17_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
/ndmg_atlases/label/Human/Yeo-7-liberal_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
/ndmg_atlases/label/Human/Yeo-7_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
amplitude_low_frequency_fluctuation:
# ALFF & f/ALFF
# Calculate Amplitude of Low Frequency Fluctuations (ALFF) and fractional ALFF (f/ALFF) for all voxels.
run: On
# space: Template or Native
target_space: [Template]
regional_homogeneity:
# ReHo
# Calculate Regional Homogeneity (ReHo) for all voxels.
run: On
# space: Template or Native
target_space: [Template]
network_centrality:
# Calculate Degree, Eigenvector Centrality, or Functional Connectivity Density.
run: On
# Full path to a NIFTI file describing the mask. Centrality will be calculated for all voxels within the mask.
template_specification_file: /cpac_templates/Mask_ABIDE_85Percent_GM.nii.gz
degree_centrality:
# Enable/Disable degree centrality by selecting the connectivity weights
# weight_options: ['Binarized', 'Weighted']
# disable this type of centrality with:
# weight_options: []
weight_options: [Binarized]
eigenvector_centrality:
# Enable/Disable eigenvector centrality by selecting the connectivity weights
# weight_options: ['Binarized', 'Weighted']
# disable this type of centrality with:
# weight_options: []
weight_options: []
local_functional_connectivity_density:
# Enable/Disable lFCD by selecting the connectivity weights
# weight_options: ['Binarized', 'Weighted']
# disable this type of centrality with:
# weight_options: []
weight_options: [Binarized, Weighted]
# OUTPUTS AND DERIVATIVES
# -----------------------
post_processing:
spatial_smoothing:
# Smooth the derivative outputs.
# Set as ['nonsmoothed'] to disable smoothing. Set as ['smoothed', 'nonsmoothed'] to get both.
#
# Options:
# ['smoothed', 'nonsmoothed']
output: [smoothed, nonsmoothed]
# Tool to use for smoothing.
# 'FSL' for FSL MultiImageMaths for FWHM provided
# 'AFNI' for AFNI 3dBlurToFWHM for FWHM provided
smoothing_method: [AFNI]
# Full Width at Half Maximum of the Gaussian kernel used during spatial smoothing.
# this is a fork point
# i.e. multiple kernels - fwhm: [4,6,8]
fwhm: [6]
z-scoring:
# z-score standardize the derivatives. This may be needed for group-level analysis.
# Set as ['raw'] to disable z-scoring. Set as ['z-scored', 'raw'] to get both.
#
# Options:
# ['z-scored', 'raw']
output: [z-scored, raw]
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