The C-PAC pipeline configuration was changed to a nested format with import capabilities in v1.8.0.

If you provide C-PAC v1.8 with a pipeline configuration file in the v1.7 format, C-PAC will attempt to update the pipeline for you, creating a directory called updated_config within your output directory, and including the following files:

  • the updated pipeline configuration file, with the same name as the original pipeline configuration file

  • the original pipeline configuration file, suffixed with a timestamp and .bak

  • any keys from the original pipeline configuration file that were not updated, suffixed with .rem

Please be sure to check that the updated pipeline configuration file configures the pipeline as intended.

The following keys are deprecated:

  • crashLogDirectory

  • output_tree

  • TR

  • fdCalc

  • reGenerateOutputs

  • runMedianAngleCorrection

  • slice_timing_pattern

  • targetAngleDeg

  • runSymbolicLinks

  • configFileTwomm

  • ref_mask_2mm

  • template_skull_for_anat_2mm

  • surface_reconstruction

See Regressors specification to manually update any of the following keys:

  • nComponents

  • nuisanceBandpassFreq

  • numRemovePrecedingFrames

  • numRemoveSubsequentFrames

  • runFrequencyFiltering

  • runFristonModel

  • runMotionSpike

  • spikeThreshold

  • smoothing_order

  • already_skullstripped

  • roiTSOutputs

The following YAML is formatted such that the keys are the pipeline configuration keys in C-PAC ≤ v1.7 and the values are a list of successively deeper keys in a C-PAC 1.8 pipeline configuration. For example,
pipelineName:
  - pipeline_setup
  - pipeline_name

indicates the change, from 1.7

pipelineName: pipline-name_value

to 1.8

pipeline_setup:
   pipeline_name: pipeline-name_value

The full list of mappings is as follows:

runOnGrid:
   - pipeline_setup
   - system_config
   - on_grid
   - run
FSLDIR:
   - pipeline_setup
   - system_config
   - FSLDIR
resourceManager:
   - pipeline_setup
   - system_config
   - on_grid
   - resource_manager
parallelEnvironment:
   - pipeline_setup
   - system_config
   - on_grid
   - SGE
   - parallel_environment
queue:
   - pipeline_setup
   - system_config
   - on_grid
   - SGE
   - queue
maximumMemoryPerParticipant:
   - pipeline_setup
   - system_config
   - maximum_memory_per_participant
maxCoresPerParticipant:
   - pipeline_setup
   - system_config
   - max_cores_per_participant
numParticipantsAtOnce:
   - pipeline_setup
   - system_config
   - num_participants_at_once
num_ants_threads:
   - pipeline_setup
   - system_config
   - num_ants_threads
num_omp_threads:
   - pipeline_setup
   - system_config
   - num_OMP_threads
pipelineName:
   - pipeline_setup
   - pipeline_name
workingDirectory:
   - pipeline_setup
   - working_directory
   - path
outputDirectory:
   - pipeline_setup
   - output_directory
   - path
run_logging:
   - pipeline_setup
   - log_directory
   - run_logging
logDirectory:
   - pipeline_setup
   - log_directory
   - path
awsOutputBucketCredentials:
   - pipeline_setup
   - Amazon-AWS
   - aws_output_bucket_credentials
s3Encryption:
   - pipeline_setup
   - Amazon-AWS
   - s3_encryption
write_func_outputs:
   - pipeline_setup
   - output_directory
   - write_func_outputs
write_debugging_outputs:
   - pipeline_setup
   - output_directory
   - write_debugging_outputs
generateQualityControlImages:
   - pipeline_setup
   - output_directory
   - quality_control
   - generate_quality_control_images
removeWorkingDir:
   - pipeline_setup
   - working_directory
   - remove_working_dir
runAnatomical:
   - anatomical_preproc
   - run
non_local_means_filtering:
   - anatomical_preproc
   - non_local_means_filtering
n4_bias_field_correction:
   - anatomical_preproc
   - n4_bias_field_correction
acpc_align:
   - anatomical_preproc
   - acpc_alignment
   - run
acpc_brainsize:
   - anatomical_preproc
   - acpc_alignment
   - brain_size
acpc_template_skull:
   - anatomical_preproc
   - acpc_alignment
   - T1w_ACPC_template
acpc_template_brain:
   - anatomical_preproc
   - acpc_alignment
   - T1w_brain_ACPC_template
acpc_run_preprocessing:
   - anatomical_preproc
   - acpc_alignment
   - run_before_preproc  # changed from string to boolean
skullstrip_option:
   - anatomical_preproc
   - brain_extraction
   - using  # values changed
unet_model:
   - anatomical_preproc
   - brain_extraction
   - UNet
   - unet_model
niworkflows_ants_template_path:
   - anatomical_preproc
   - brain_extraction
   - niworkflows-ants
   - template_path
niworkflows_ants_mask_path:
   - anatomical_preproc
   - brain_extraction
   - niworkflows-ants
   - mask_path
niworkflows_ants_regmask_path:
   - anatomical_preproc
   - brain_extraction
   - niworkflows-ants
   - regmask_path
skullstrip_mask_vol:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - mask_vol
skullstrip_shrink_factor:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - shrink_factor
skullstrip_var_shrink_fac:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - var_shrink_fac
skullstrip_shrink_factor_bot_lim:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - shrink_factor_bot_lim
skullstrip_avoid_vent:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - avoid_vent
skullstrip_n_iterations:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - n_iterations
skullstrip_pushout:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - pushout
skullstrip_touchup:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - touchup
skullstrip_fill_hole:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - fill_hole
skullstrip_NN_smooth:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - NN_smooth
skullstrip_smooth_final:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - smooth_final
skullstrip_avoid_eyes:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - avoid_eyes
skullstrip_use_edge:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - use_edge
skullstrip_exp_frac:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - exp_frac
skullstrip_push_to_edge:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - push_to_edge
skullstrip_use_skull:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - use_skull
skullstrip_perc_int:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - perc_int
skullstrip_max_inter_iter:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - max_inter_iter
skullstrip_fac:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - fac
skullstrip_blur_fwhm:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - blur_fwhm
skullstrip_monkey:
   - anatomical_preproc
   - brain_extraction
   - AFNI-3dSkullStrip
   - monkey
bet_frac:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - frac
bet_mask_boolean:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - mask_boolean
bet_mesh_boolean:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - mesh_boolean
bet_outline:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - outline
bet_padding:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - padding
bet_radius:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - radius
bet_reduce_bias:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - reduce_bias
bet_remove_eyes:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - remove_eyes
bet_robust:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - robust
bet_skull:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - skull
bet_surfaces:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - surfaces
bet_threshold:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - threshold
bet_vertical_gradient:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - vertical_gradient
run_longitudinal:
   - longitudinal_template_generation
   - run
longitudinal_template_average_method:
   - longitudinal_template_generation
   - average_method
longitudinal_template_dof:
   - longitudinal_template_generation
   - dof
longitudinal_template_interp:
   - longitudinal_template_generation
   - interp
longitudinal_template_cost:
   - longitudinal_template_generation
   - cost
longitudinal_template_thread_pool:
   - longitudinal_template_generation
   - thread_pool
longitudinal_template_convergence_threshold:
   - longitudinal_template_generation
   - convergence_threshold
resolution_for_anat:
   - registration_workflows
   - anatomical_registration
   - resolution_for_anat
template_brain_only_for_anat:
   - registration_workflows
   - anatomical_registration
   - T1w_brain_template
template_skull_for_anat:
   - registration_workflows
   - anatomical_registration
   - T1w_template
template_brain_mask_for_anat:
   - registration_workflows
   - anatomical_registration
   - T1w_brain_template_mask
regOption:
   - registration_workflows
   - anatomical_registration
   - registration
   - using
ANTs_para_T1_registration:
   - registration_workflows
   - anatomical_registration
   - registration
   - ANTs
   - T1_registration
ANTs_para_EPI_registration:
   - registration_workflows
   - functional_registration
   - EPI_registration
   - ANTs
   - parameters
use_lesion_mask:
   - registration_workflows
   - anatomical_registration
   - registration
   - ANTs
   - use_lesion_mask
fsl_linear_reg_only:
   - registration_workflows
   - anatomical_registration
   - registration
   - using  # changed from boolean to string
fnirtConfig:
   - registration_workflows
   - anatomical_registration
   - registration
   - FSL-FNIRT
   - fnirt_config
# --- ALSO ---
# fnirtConfig:
#    - registration_workflows
#    - functional_registration
#    - EPI_registration
#    - FSL-FNIRT
#    - fnirt_config
ref_mask:
   - registration_workflows
   - anatomical_registration
   - registration
   - FSL-FNIRT
   - ref_mask
regWithSkull:
   - registration_workflows
   - anatomical_registration
   - reg_with_skull
runSegmentationPreprocessing:
   - segmentation
   - run
segmentation_method:
   - segmentation
   - tissue_segmentation
   - using  # values changed
ANTs_prior_seg_template_brain_list:
   - segmentation
   - tissue_segmentation
   - ANTs_Prior_Based
   - template_brain_list
ANTs_prior_seg_template_segmentation_list:
   - segmentation
   - tissue_segmentation
   - ANTs_Prior_Based
   - template_segmentation_list
ANTs_prior_seg_CSF_label:
   - segmentation
   - tissue_segmentation
   - ANTs_Prior_Based
   - CSF_label
ANTs_prior_seg_left_GM_label:
   - segmentation
   - tissue_segmentation
   - ANTs_Prior_Based
   - left_GM_label
ANTs_prior_seg_right_GM_label:
   - segmentation
   - tissue_segmentation
   - ANTs_Prior_Based
   - right_GM_label
ANTs_prior_seg_left_WM_label:
   - segmentation
   - tissue_segmentation
   - ANTs_Prior_Based
   - left_WM_label
ANTs_prior_seg_right_WM_label:
   - segmentation
   - tissue_segmentation
   - ANTs_Prior_Based
   - right_WM_label
template_based_segmentation:
   - segmentation
   - tissue_segmentation
   - Template_Based
   - template_for_segmentation  # removed 'None' from valid options; use empty list for 'None'
template_based_segmentation_WHITE:
   - segmentation
   - tissue_segmentation
   - Template_Based
   - WHITE
template_based_segmentation_GRAY:
   - segmentation
   - tissue_segmentation
   - Template_Based
   - GRAY
template_based_segmentation_CSF:
   - segmentation
   - tissue_segmentation
   - Template_Based
   - CSF
seg_use_priors:
   - segmentation
   - tissue_segmentation
   - FSL-FAST
   - use_priors
   - run
priors_path:
   - segmentation
   - tissue_segmentation
   - FSL-FAST
   - use_priors
   - priors_path
PRIORS_WHITE:
   - segmentation
   - tissue_segmentation
   - FSL-FAST
   - use_priors
   - WM_path
PRIORS_GRAY:
   - segmentation
   - tissue_segmentation
   - FSL-FAST
   - use_priors
   - GM_path
PRIORS_CSF:
   - segmentation
   - tissue_segmentation
   - FSL-FAST
   - use_priors
   - CSF_path
seg_use_threshold:
   - segmentation
   - tissue_segmentation
   - FSL-FAST
   - thresholding
   - use  # values changed
seg_CSF_threshold_value:
   - segmentation
   - tissue_segmentation
   - FSL-FAST
   - thresholding
   - Custom
   - CSF_threshold_value
seg_WM_threshold_value:
   - segmentation
   - tissue_segmentation
   - FSL-FAST
   - thresholding
   - Custom
   - WM_threshold_value
seg_GM_threshold_value:
   - segmentation
   - tissue_segmentation
   - FSL-FAST
   - thresholding
   - Custom
   - GM_threshold_value
seg_csf_use_erosion:
   - nuisance_corrections
   - 2-nuisance_regression
   - regressor_masks
   - erode_csf
   - run
brain_use_erosion:
   - nuisance_corrections
   - 2-nuisance_regression
   - regressor_masks
   - erode_anatomical_brain_mask
   - run
brain_mask_erosion_prop:
   - nuisance_corrections
   - 2-nuisance_regression
   - regressor_masks
   - erode_anatomical_brain_mask
   - brain_mask_erosion_prop
brain_mask_erosion_mm:
   - nuisance_corrections
   - 2-nuisance_regression
   - regressor_masks
   - erode_anatomical_brain_mask
   - brain_mask_erosion_mm
brain_erosion_mm:
   - nuisance_corrections
   - 2-nuisance_regression
   - regressor_masks
   - erode_anatomical_brain_mask
   - brain_erosion_mm
csf_erosion_prop:
   - nuisance_corrections
   - 2-nuisance_regression
   - regressor_masks
   - erode_csf
   - csf_erosion_prop
csf_mask_erosion_mm:
   - nuisance_corrections
   - 2-nuisance_regression
   - regressor_masks
   - erode_csf
   - csf_mask_erosion_mm
csf_erosion_mm:
   - nuisance_corrections
   - 2-nuisance_regression
   - regressor_masks
   - erode_csf
   - csf_erosion_mm
seg_wm_use_erosion:
   - nuisance_corrections
   - 2-nuisance_regression
   - regressor_masks
   - erode_wm
   - run
wm_erosion_prop:
   - nuisance_corrections
   - 2-nuisance_regression
   - regressor_masks
   - erode_wm
   - wm_erosion_prop
wm_mask_erosion_mm:
   - nuisance_corrections
   - 2-nuisance_regression
   - regressor_masks
   - erode_wm
   - wm_mask_erosion_mm
wm_erosion_mm:
   - nuisance_corrections
   - 2-nuisance_regression
   - regressor_masks
   - erode_wm
   - wm_erosion_mm
seg_gm_use_erosion:
   - nuisance_corrections
   - 2-nuisance_regression
   - regressor_masks
   - erode_gm
   - run
gm_erosion_prop:
   - nuisance_corrections
   - 2-nuisance_regression
   - regressor_masks
   - erode_gm
   - gm_erosion_prop
gm_mask_erosion_mm:
   - nuisance_corrections
   - 2-nuisance_regression
   - regressor_masks
   - erode_gm
   - gm_mask_erosion_mm
gm_erosion_mm:
   - nuisance_corrections
   - 2-nuisance_regression
   - regressor_masks
   - erode_gm
   - gm_erosion_mm
runFunctional:
   - functional_preproc
   - run
runScaling:
   - functional_preproc
   - scaling
   - run
scaling_factor:
   - functional_preproc
   - scaling
   - scaling_factor
runMotionStatisticsFirst:
   - functional_preproc
   - motion_estimates_and_correction
   - calculate_motion_first
motion_correction:
   - functional_preproc
   - motion_estimates_and_correction
   - motion_correction
   - using
motion_correction_reference:
   - functional_preproc
   - motion_estimates_and_correction
   - motion_correction
   - motion_correction_reference
motion_correction_reference_volume:
   - functional_preproc
   - motion_estimates_and_correction
   - motion_correction
   - motion_correction_reference_volume
functional_volreg_twopass:
   - functional_preproc
   - motion_estimates_and_correction
   - motion_correction
   - AFNI-3dvolreg
   - functional_volreg_twopass
motion_estimate_filter:
   - functional_preproc
   - motion_estimates_and_correction
   - motion_estimate_filter
runDespike:
   - functional_preproc
   - despiking
   - run
slice_timing_correction:
   - functional_preproc
   - slice_timing_correction
   - run
startIdx:
   - functional_preproc
   - truncation
   - start_tr
stopIdx:
   - functional_preproc
   - truncation
   - stop_tr
distortion_correction:
   - functional_preproc
   - distortion_correction
   - using  # removed 'None' from valid options; use empty list for 'None'
fmap_distcorr_skullstrip:
   - functional_preproc
   - distortion_correction
   - PhaseDiff
   - fmap_skullstrip_option
fmap_distcorr_frac:
   - functional_preproc
   - distortion_correction
   - PhaseDiff
   - fmap_skullstrip_BET_frac
fmap_distcorr_threshold:
   - functional_preproc
   - distortion_correction
   - PhaseDiff
   - fmap_skullstrip_AFNI_threshold
runRegisterFuncToAnat:
   - registration_workflows
   - functional_registration
   - coregistration
   - run
functional_registration:
   - registration_workflows
   - functional_registration
runBBReg:
   - registration_workflows
   - functional_registration
   - coregistration
   - boundary_based_registration
   - run
boundaryBasedRegistrationSchedule:
   - registration_workflows
   - functional_registration
   - coregistration
   - boundary_based_registration
   - bbr_schedule
anatRegANTSinterpolation:
   - registration_workflows
   - anatomical_registration
   - registration
   - ANTs
   - interpolation
anatRegFSLinterpolation:
   - registration_workflows
   - anatomical_registration
   - registration
   - FSL-FNIRT
   - interpolation
funcRegANTSinterpolation:
   - registration_workflows
   - functional_registration
   - func_registration_to_template
   - ANTs_pipelines
   - interpolation
funcRegFSLinterpolation:
   - registration_workflows
   - functional_registration
   - EPI_registration
   - FSL-FNIRT
   - interpolation
func_reg_input:
   - registration_workflows
   - functional_registration
   - coregistration
   - func_input_prep
   - input
func_reg_input_volume:
   - registration_workflows
   - functional_registration
   - coregistration
   - func_input_prep
   - Selected Functional Volume
   - func_reg_input_volume
n4_correct_func_reg_input:
   - registration_workflows
   - functional_registration
   - coregistration
   - func_input_prep
   - Mean Functional
   - n4_correct_func
functionalMasking:
   - functional_preproc
   - func_masking
   - using  # values changed
bold_bet_functional_mean_boolean:
   - functional_preproc
   - func_masking
   - FSL-BET
   - functional_mean_boolean
bold_bet_frac:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - frac
bold_bet_mesh_boolean:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - mesh_boolean
bold_bet_outline:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - outline
bold_bet_padding:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - padding
bold_bet_radius:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - radius
bold_bet_reduce_bias:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - reduce_bias
bold_bet_remove_eyes:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - remove_eyes
bold_bet_robust:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - robust
bold_bet_skull:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - skull
bold_bet_surfaces:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - surfaces
bold_bet_threshold:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - threshold
bold_bet_vertical_gradient:
   - anatomical_preproc
   - brain_extraction
   - FSL-BET
   - vertical_gradient
anatomical_mask_dilation:
   - functional_preproc
   - func_masking
   - Anatomical_Refined
   - anatomical_mask_dilation
runRegisterFuncToTemplate:
   - registration_workflows
   - functional_registration
   - func_registration_to_template
   - target_template
   - using  # removed 'Off' from valid options; use empty list for 'Off'
resolution_for_func_preproc:
   - registration_workflows
   - functional_registration
   - func_registration_to_template
   - output_resolution
   - func_preproc_outputs
resolution_for_func_derivative:
   - registration_workflows
   - functional_registration
   - func_registration_to_template
   - output_resolution
   - func_derivative_outputs
template_for_resample:
   - registration_workflows
   - functional_registration
   - func_registration_to_template
   - target_template
   - T1_template
   - T1w_template_for_resample
# --- ALSO ---
# template_for_resample:
#   - registration_workflows
#   - functional_registration
#   - func_registration_to_template
#   - target_template
#   - EPI_template
#   - EPI_template_for_resample
template_brain_only_for_func:
   - registration_workflows
   - functional_registration
   - func_registration_to_template
   - target_template
   - T1_template
   - T1w_brain_template_funcreg
template_skull_for_func:
   - registration_workflows
   - functional_registration
   - func_registration_to_template
   - target_template
   - T1_template
   - T1w_template_funcreg
template_brain_mask_for_func:
   - registration_workflows
   - functional_registration
   - func_registration_to_template
   - target_template
   - T1_template
   - T1w_brain_template_mask_funcreg
template_epi:
   - registration_workflows
   - functional_registration
   - func_registration_to_template
   - target_template
   - EPI_template
   - EPI_template_funcreg
identityMatrix:
   - registration_workflows
   - functional_registration
   - EPI_registration
   - FSL-FNIRT
   - identity_matrix
runICA:
   - nuisance_corrections
   - 1-ICA-AROMA
   - run
aroma_denoise_type:
   - nuisance_corrections
   - 1-ICA-AROMA
   - denoising_type
runNuisance:
   - nuisance_corrections
   - 2-nuisance_regression
   - run
lateral_ventricles_mask:
   - nuisance_corrections
   - 2-nuisance_regression
   - lateral_ventricles_mask
Regressors:
   - nuisance_corrections
   - 2-nuisance_regression
   - Regressors
filtering_order:
   - nuisance_corrections
   - 2-nuisance_regression
   - bandpass_filtering_order
runROITimeseries:
   - timeseries_extraction
   - run
realignment:
   - timeseries_extraction
   - realignment
tsa_roi_paths:
   - timeseries_extraction
   - tse_roi_paths
runSCA:
   - seed_based_correlation_analysis
   - run
sca_roi_paths:
   - seed_based_correlation_analysis
   - sca_roi_paths
mrsNorm:
   - seed_based_correlation_analysis
   - norm_timeseries_for_DR
runVMHC:
   - voxel_mirrored_homotopic_connectivity
   - run
template_symmetric_brain_only:
   - voxel_mirrored_homotopic_connectivity
   - symmetric_registration
   - T1w_brain_template_symmetric
template_symmetric_brain_for_resample:
   - voxel_mirrored_homotopic_connectivity
   - symmetric_registration
   - T1w_brain_template_symmetric_for_resample
template_symmetric_skull:
   - voxel_mirrored_homotopic_connectivity
   - symmetric_registration
   - T1w_template_symmetric
template_symmetric_skull_for_resample:
   - voxel_mirrored_homotopic_connectivity
   - symmetric_registration
   - T1w_template_symmetric_for_resample
dilated_symmetric_brain_mask:
   - voxel_mirrored_homotopic_connectivity
   - symmetric_registration
   - dilated_symmetric_brain_mask
dilated_symmetric_brain_mask_for_resample:
   - voxel_mirrored_homotopic_connectivity
   - symmetric_registration
   - dilated_symmetric_brain_mask_for_resample
runALFF:
   - amplitude_low_frequency_fluctuation
   - run
highPassFreqALFF:
   - amplitude_low_frequency_fluctuation
   - highpass_cutoff
lowPassFreqALFF:
   - amplitude_low_frequency_fluctuation
   - lowpass_cutoff
runReHo:
   - regional_homogeneity
   - run
clusterSize:
   - regional_homogeneity
   - cluster_size
runNetworkCentrality:
   - network_centrality
   - run
templateSpecificationFile:
   - network_centrality
   - template_specification_file
degWeightOptions:
   - network_centrality
   - degree_centrality
   - weight_options  # changed from boolean to string
degCorrelationThresholdOption:
   - network_centrality
   - degree_centrality
   - correlation_threshold_option
degCorrelationThreshold:
   - network_centrality
   - degree_centrality
   - correlation_threshold
eigWeightOptions:
   - network_centrality
   - eigenvector_centrality
   - weight_options  # changed from boolean to string
eigCorrelationThresholdOption:
   - network_centrality
   - eigenvector_centrality
   - correlation_threshold_option
eigCorrelationThreshold:
   - network_centrality
   - eigenvector_centrality
   - correlation_threshold
lfcdWeightOptions:
   - network_centrality
   - local_functional_connectivity_density
   - weight_options  # changed from boolean to string
lfcdCorrelationThresholdOption:
   - network_centrality
   - local_functional_connectivity_density
   - correlation_threshold_option
lfcdCorrelationThreshold:
   - network_centrality
   - local_functional_connectivity_density
   - correlation_threshold
memoryAllocatedForDegreeCentrality:
   - network_centrality
   - memory_allocation
run_smoothing:
   - post_processing
   - spatial_smoothing
   - output  # changed from boolean to string
smoothing_method:
   - post_processing
   - spatial_smoothing
   - smoothing_method
fwhm:
   - post_processing
   - spatial_smoothing
   - fwhm
runZScoring:
   - post_processing
   - z-scoring
   - output  # changed from boolean to string
run_freesurfer:
   - surface_analysis
   - freesurfer
   - run_reconall
run_pypeer:
   - PyPEER
   - run
peer_eye_scan_names:
   - PyPEER
   - eye_scan_names
peer_data_scan_names:
   - PyPEER
   - data_scan_names
eye_mask_path:
   - PyPEER
   - eye_mask_path
peer_stimulus_path:
   - PyPEER
   - stimulus_path
peer_gsr:
   - PyPEER
   - minimal_nuisance_correction
   - peer_gsr
peer_scrub:
   - PyPEER
   - minimal_nuisance_correction
   - peer_scrub
peer_scrub_thresh:
   - PyPEER
   - minimal_nuisance_correction
   - scrub_thresh
n4_correct_mean_EPI:
   - registration_workflows
   - functional_registration
   - coregistration
   - func_input_prep
   - Mean Functional
   - n4_correct_func
anatomical_preproc:
   - anatomical_preproc
   - run
runRegisterFuncToEPI:
   - registration_workflows
   - functional_registration
   - func_registration_to_template
   - target_template
   - using  # moved from its own boolean key to a string value
ANTs_prior_based_segmentation:
   - segmentation
   - tissue_segmentation
   - using  # moved from its own boolean key to a string value
bold_bet_mask_boolean:
   - functional_preproc
   - func_masking
   - FSL-BET
   - functional_mean_boolean