%YAML 1.1 --- # CPAC Pipeline Configuration YAML file # Version 1.8.3 # # http://fcp-indi.github.io for more info. # # Pipeline config "Default (2)", version GUI-0 # Tue May 10 2022 11:51:35 GMT+0100 (British Summer Time) # # Tip: This file can be edited manually with a text editor for quick modifications. pipeline_setup: pipeline_name: cpac-w_fmriprep-derivs output_directory: path: /output source_outputs_dir: None pull_source_once: true write_func_outputs: false write_debugging_outputs: false output_tree: default quality_control: generate_quality_control_images: true generate_xcpqc_files: false working_directory: path: /tmp remove_working_dir: true log_directory: run_logging: true path: /logs crash_log_directory: path: /crash system_config: random_seed: null on_grid: run: false resource_manager: SGE SGE: parallel_environment: mpi_smp queue: all.q maximum_memory_per_participant: 1 max_cores_per_participant: 1 num_ants_threads: 1 num_OMP_threads: 1 num_participants_at_once: 1 FSLDIR: /usr/share/fsl/5.0 Amazon-AWS: aws_output_bucket_credentials: null s3_encryption: false Debugging: verbose: true timeseries_extraction: run: true tse_roi_paths: /cpac_templates/PNAS_Smith09_rsn10.nii.gz: SpatialReg /ndmg_atlases/label/Human/Yeo-17_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/CAPRSC_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /cpac_templates/ho_mask_pad.nii.gz: Avg /cpac_templates/CC400.nii.gz: Avg /cpac_templates/CC200.nii.gz: Avg /ndmg_atlases/label/Human/DesikanKlein_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/DKT_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Yeo-7_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/HarvardOxfordsub-maxprob-thr25_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/AAL_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/MICCAI_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Glasser_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/HarvardOxfordcort-maxprob-thr25_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /cpac_templates/rois_3mm.nii.gz: Avg /ndmg_atlases/label/Human/Slab907_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Yeo-17-liberal_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Desikan_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /cpac_templates/aal_mask_pad.nii.gz: Avg /ndmg_atlases/label/Human/Brodmann_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Yeo-7-liberal_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /cpac_templates/tt_mask_pad.nii.gz: Avg /ndmg_atlases/label/Human/Schaefer400_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Juelich_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Schaefer300_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Schaefer1000_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Talairach_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Schaefer200_space-MNI152NLin6_res-1x1x1.nii.gz: Avg realignment: ROI_to_func connectivity_matrix: using: - Nilearn measure: - Pearson - Partial segmentation: run: false tissue_segmentation: using: - FSL-FAST FSL-FAST: thresholding: use: Auto Custom: CSF_threshold_value: 0.95 WM_threshold_value: 0.95 GM_threshold_value: 0.95 use_priors: run: true priors_path: $FSLDIR/data/standard/tissuepriors/2mm WM_path: $priors_path/avg152T1_white_bin.nii.gz GM_path: $priors_path/avg152T1_gray_bin.nii.gz CSF_path: $priors_path/avg152T1_csf_bin.nii.gz Template_Based: template_for_segmentation: - T1_Template WHITE: $FSLDIR/data/standard/tissuepriors/2mm/avg152T1_white_bin.nii.gz GRAY: $FSLDIR/data/standard/tissuepriors/2mm/avg152T1_gray_bin.nii.gz CSF: $FSLDIR/data/standard/tissuepriors/2mm/avg152T1_csf_bin.nii.gz ANTs_Prior_Based: template_brain_list: - /cpac_templates/MacaqueYerkes19_T1w_0.5mm_desc-JLC_T1w_brain.nii.gz - >- /cpac_templates/J_Macaque_11mo_atlas_nACQ_194x252x160space_0.5mm_desc-JLC_T1w_brain.nii.gz template_segmentation_list: - /cpac_templates/MacaqueYerkes19_T1w_0.5mm_desc-JLC_Segmentation.nii.gz - >- /cpac_templates/J_Macaque_11mo_atlas_nACQ_194x252x160space_0.5mm_desc-JLC_Segmentation.nii.gz CSF_label: - 24 GM_label: - 3 - 42 WM_label: - 2 - 41 FreeSurfer: erode: 0 CSF_label: - 24 GM_label: - 3 - 42 WM_label: - 2 - 41 longitudinal_template_generation: run: false average_method: median dof: 12 interp: trilinear cost: corratio thread_pool: 2 convergence_threshold: -1 network_centrality: run: true memory_allocation: 1 template_specification_file: /cpac_templates/Mask_ABIDE_85Percent_GM.nii.gz degree_centrality: weight_options: - Binarized - Weighted correlation_threshold_option: Sparsity threshold correlation_threshold: 0.001 eigenvector_centrality: weight_options: - Weighted correlation_threshold_option: Sparsity threshold correlation_threshold: 0.001 local_functional_connectivity_density: weight_options: - Binarized - Weighted correlation_threshold_option: Correlation threshold correlation_threshold: 0.6 PyPEER: run: false eye_scan_names: [] data_scan_names: [] eye_mask_path: '$FSLDIR/data/standard/MNI152_T1_${func_resolution}_eye_mask.nii.gz' stimulus_path: None minimal_nuisance_correction: peer_gsr: false peer_scrub: false scrub_thresh: 0.2 registration_workflows: anatomical_registration: run: false resolution_for_anat: 2mm T1w_brain_template: >- /usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz T1w_template: '/usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz' T1w_brain_template_mask: >- /usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz reg_with_skull: true registration: using: - ANTS ANTs: use_lesion_mask: false T1_registration: - collapse-output-transforms: 0 - dimensionality: 3 - initial-moving-transform: initializationFeature: 0 - transforms: - Rigid: gradientStep: 0.1 metric: type: MI metricWeight: 1 numberOfBins: 32 samplingStrategy: Regular samplingPercentage: 0.25 convergence: iteration: 1000x500x250x100 convergenceThreshold: 1.e-8 convergenceWindowSize: 10 smoothing-sigmas: 3.0x2.0x1.0x0.0 shrink-factors: 8x4x2x1 use-histogram-matching: true - Affine: gradientStep: 0.1 metric: type: MI metricWeight: 1 numberOfBins: 32 samplingStrategy: Regular samplingPercentage: 0.25 convergence: iteration: 1000x500x250x100 convergenceThreshold: 1.e-8 convergenceWindowSize: 10 smoothing-sigmas: 3.0x2.0x1.0x0.0 shrink-factors: 8x4x2x1 use-histogram-matching: true - SyN: shrink-factors: 6x4x2x1 updateFieldVarianceInVoxelSpace: 3 smoothing-sigmas: 3.0x2.0x1.0x0.0 totalFieldVarianceInVoxelSpace: 0 use-histogram-matching: true winsorize-image-intensities: lowerQuantile: 0.01 upperQuantile: 0.99 metric: type: CC metricWeight: 1 radius: 4 convergence: iteration: 100x100x70x20 convergenceThreshold: 1.e-9 convergenceWindowSize: 15 gradientStep: 0.1 interpolation: LanczosWindowedSinc FSL-FNIRT: identity_matrix: /usr/share/fsl/5.0/etc/flirtsch/ident.mat FNIRT_T1w_brain_template: None interpolation: sinc T1w_template_res-2: /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm.nii.gz ref_mask: >- /usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask_dil.nii.gz ref_resolution: 2mm FNIRT_T1w_template: None fnirt_config: T1_2_MNI152_2mm ref_mask_res-2: /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz overwrite_transform: run: false using: FSL functional_registration: coregistration: using: FSL interpolation: trilinear input: brain run: false reference: brain cost: corratio arguments: None boundary_based_registration: run: - true bbr_schedule: /usr/share/fsl/5.0/etc/flirtsch/bbr.sch reference: whole-head bbr_wm_map: probability_map bbr_wm_mask_args: '-thr 0.5 -bin' dof: 6 func_input_prep: reg_with_skull: false input: - Mean_Functional Mean Functional: n4_correct_func: false Selected Functional Volume: func_reg_input_volume: 0 EPI_registration: run: false using: - ANTS EPI_template: 's3://fcp-indi/resources/cpac/resources/epi_hbn.nii.gz' EPI_template_mask: None ANTs: parameters: - collapse-output-transforms: 0 - dimensionality: 3 - initial-moving-transform: initializationFeature: 0 - transforms: - Rigid: gradientStep: 0.1 metric: type: MI metricWeight: 1 numberOfBins: 32 samplingStrategy: Regular samplingPercentage: 0.25 convergence: iteration: 1000x500x250x100 convergenceThreshold: 1.e-8 convergenceWindowSize: 10 smoothing-sigmas: 3.0x2.0x1.0x0.0 shrink-factors: 8x4x2x1 use-histogram-matching: true - Affine: gradientStep: 0.1 metric: type: MI metricWeight: 1 numberOfBins: 32 samplingStrategy: Regular samplingPercentage: 0.25 convergence: iteration: 1000x500x250x100 convergenceThreshold: 1.e-8 convergenceWindowSize: 10 smoothing-sigmas: 3.0x2.0x1.0x0.0 shrink-factors: 8x4x2x1 use-histogram-matching: true - SyN: shrink-factors: 6x4x2x1 updateFieldVarianceInVoxelSpace: 3 smoothing-sigmas: 3.0x2.0x1.0x0.0 totalFieldVarianceInVoxelSpace: 0 use-histogram-matching: true winsorize-image-intensities: lowerQuantile: 0.01 upperQuantile: 0.99 metric: type: CC metricWeight: 1 radius: 4 convergence: iteration: 100x100x70x20 convergenceThreshold: 1.e-9 convergenceWindowSize: 15 gradientStep: 0.1 interpolation: LanczosWindowedSinc FSL-FNIRT: fnirt_config: T1_2_MNI152_2mm interpolation: sinc identity_matrix: /usr/share/fsl/5.0/etc/flirtsch/ident.mat func_registration_to_template: run: true run_EPI: false output_resolution: func_preproc_outputs: 3mm func_derivative_outputs: 3mm target_template: using: - T1_template T1_template: T1w_brain_template_funcreg: >- /usr/share/fsl/5.0/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz T1w_template_funcreg: '/usr/share/fsl/5.0/data/standard/MNI152_T1_${func_resolution}.nii.gz' T1w_brain_template_mask_funcreg: >- /usr/share/fsl/5.0/data/standard/MNI152_T1_${func_resolution}_brain_mask.nii.gz T1w_template_for_resample: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz EPI_template: EPI_template_funcreg: 's3://fcp-indi/resources/cpac/resources/epi_hbn.nii.gz' EPI_template_mask_funcreg: None EPI_template_for_resample: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz ANTs_pipelines: interpolation: LanczosWindowedSinc FNIRT_pipelines: interpolation: sinc identity_matrix: /usr/share/fsl/5.0/etc/flirtsch/ident.mat apply_transform: using: default surface_analysis: freesurfer: run: false reconall_args: None freesurfer_dir: None post_freesurfer: smooth_fwhm: 2 high_res_mesh: 164 run: false gray_ordinates_res: 2 subcortical_gray_labels: >- /opt/dcan-tools/pipeline/global/config/FreeSurferSubcorticalLabelTableLut.txt freesurfer_labels: /opt/dcan-tools/pipeline/global/config/FreeSurferAllLut.txt surf_atlas_dir: /opt/dcan-tools/pipeline/global/templates/standard_mesh_atlases low_res_mesh: 32 gray_ordinates_dir: /opt/dcan-tools/pipeline/global/templates/91282_Greyordinates fmri_res: 2 regional_homogeneity: run: true cluster_size: 27 post_processing: spatial_smoothing: output: - smoothed smoothing_method: - FSL fwhm: - 4 z-scoring: output: - z-scored seed_based_correlation_analysis: run: true sca_roi_paths: /cpac_templates/PNAS_Smith09_rsn10.nii.gz: DualReg /cpac_templates/CC400.nii.gz: 'Avg, MultReg' /cpac_templates/ez_mask_pad.nii.gz: 'Avg, MultReg' /cpac_templates/aal_mask_pad.nii.gz: 'Avg, MultReg' /cpac_templates/CC200.nii.gz: 'Avg, MultReg' /cpac_templates/tt_mask_pad.nii.gz: 'Avg, MultReg' /cpac_templates/ho_mask_pad.nii.gz: 'Avg, MultReg' /cpac_templates/rois_3mm.nii.gz: 'Avg, MultReg' norm_timeseries_for_DR: true nuisance_corrections: 1-ICA-AROMA: run: - false denoising_type: nonaggr 2-nuisance_regression: run: - true create_regressors: false Regressors: - Name: default Motion: include_delayed: true include_squared: true include_delayed_squared: true aCompCor: summary: method: DetrendPC components: 5 tissues: - WhiteMatter - CerebrospinalFluid extraction_resolution: 2 CerebrospinalFluid: summary: Mean extraction_resolution: 2 erode_mask: true GlobalSignal: summary: Mean PolyOrt: degree: 2 Bandpass: bottom_frequency: 0.01 top_frequency: 0.1 method: default - Name: defaultNoGSR Motion: include_delayed: true include_squared: true include_delayed_squared: true aCompCor: summary: method: DetrendPC components: 5 tissues: - WhiteMatter - CerebrospinalFluid extraction_resolution: 2 CerebrospinalFluid: summary: Mean extraction_resolution: 2 erode_mask: true PolyOrt: degree: 2 Bandpass: bottom_frequency: 0.01 top_frequency: 0.1 method: default lateral_ventricles_mask: >- $FSLDIR/data/atlases/HarvardOxford/HarvardOxford-lateral-ventricles-thr25-2mm.nii.gz bandpass_filtering_order: After regressor_masks: erode_anatomical_brain_mask: run: false brain_mask_erosion_prop: 0 brain_mask_erosion_mm: 30 brain_erosion_mm: 0 erode_csf: run: false csf_erosion_prop: 0 csf_mask_erosion_mm: 30 csf_erosion_mm: 0 erode_wm: run: false wm_erosion_prop: 0.6 wm_mask_erosion_mm: 0 wm_erosion_mm: 0 erode_gm: run: false gm_erosion_prop: 0.6 gm_mask_erosion_mm: 30 gm_erosion_mm: 0 amplitude_low_frequency_fluctuation: run: true highpass_cutoff: - 0.01 lowpass_cutoff: - 0.1 voxel_mirrored_homotopic_connectivity: run: true symmetric_registration: T1w_brain_template_symmetric: >- $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_symmetric.nii.gz T1w_brain_template_symmetric_for_resample: $FSLDIR/data/standard/MNI152_T1_1mm_brain_symmetric.nii.gz T1w_template_symmetric: '$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_symmetric.nii.gz' T1w_template_symmetric_for_resample: $FSLDIR/data/standard/MNI152_T1_1mm_symmetric.nii.gz dilated_symmetric_brain_mask: >- $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask_symmetric_dil.nii.gz dilated_symmetric_brain_mask_for_resample: $FSLDIR/data/standard/MNI152_T1_1mm_brain_mask_symmetric_dil.nii.gz functional_preproc: distortion_correction: run: - false using: - PhaseDiff - Blip PhaseDiff: fmap_skullstrip_option: BET fmap_skullstrip_BET_frac: 0.5 fmap_skullstrip_AFNI_threshold: 0.6 Blip-FSL-TOPUP: miter: 5 numprec: double lambda: 1 scale: 0 minmet: 0 regmod: bending_energy estmov: 1 subsamp: 1 interp: spline fwhm: 8 ssqlambda: 1 warpres: 10 regrid: 1 splineorder: 3 despiking: run: - false motion_estimates_and_correction: run: false motion_estimates: calculate_motion_first: false calculate_motion_after: false motion_correction: using: - 3dvolreg AFNI-3dvolreg: functional_volreg_twopass: false motion_correction_reference: - mean motion_correction_reference_volume: 0 motion_estimate_filter: run: - false filter_type: notch filter_order: 4 breathing_rate_min: null breathing_rate_max: null center_frequency: null filter_bandwidth: null lowpass_cutoff: null slice_timing_correction: run: - false tpattern: None tzero: None scaling: run: false scaling_factor: 10 truncation: start_tr: 0 stop_tr: None run: false normalize_func: run: false generate_func_mean: run: false func_masking: using: - AFNI FSL-BET: functional_mean_thr: run: false threshold_value: 98 outline: false functional_mean_bias_correction: false surfaces: false functional_mean_boolean: false threshold: false frac: 0.3 padding: false robust: false radius: 0 reduce_bias: false mesh_boolean: false vertical_gradient: 0 remove_eyes: false skull: false FSL_AFNI: bold_ref: >- /code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz brain_mask: >- /code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz brain_probseg: >- /code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_res-01_label-brain_probseg.nii.gz Anatomical_Refined: anatomical_mask_dilation: false apply_func_mask_in_native_space: false anatomical_preproc: run: false run_t2: false non_local_means_filtering: run: - false noise_model: Gaussian n4_bias_field_correction: run: - false shrink_factor: 2 t1t2_bias_field_correction: run: false BiasFieldSmoothingSigma: 5 acpc_alignment: FOV_crop: robustfov brain_size: 150 run: false run_before_preproc: false align_brain_mask: false T2w_brain_ACPC_template: None T1w_brain_ACPC_template: /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz acpc_target: whole-head T2w_ACPC_template: None T1w_ACPC_template: /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm.nii.gz brain_extraction: run: false using: - 3dSkullStrip AFNI-3dSkullStrip: mask_vol: false shrink_factor: 0.6 use_skull: false smooth_final: 20 n_iterations: 250 fac: 1 var_shrink_fac: false avoid_eyes: false NN_smooth: 72 blur_fwhm: 0 exp_frac: 0.1 monkey: false pushout: false use_edge: false max_inter_iter: 4 perc_int: 0 touchup: false push_to_edge: false fill_hole: 10 shrink_factor_bot_lim: 0.4 avoid_vent: false FSL-BET: outline: false surfaces: false threshold: false frac: 0.5 padding: false robust: false radius: 0 reduce_bias: false mask_boolean: false mesh_boolean: false vertical_gradient: 0 remove_eyes: false skull: false UNet: unet_model: 's3://fcp-indi/resources/cpac/resources/Site-All-T-epoch_36.model' niworkflows-ants: template_path: /ants_template/oasis/T_template0.nii.gz mask_path: /ants_template/oasis/T_template0_BrainCerebellumProbabilityMask.nii.gz regmask_path: /ants_template/oasis/T_template0_BrainCerebellumRegistrationMask.nii.gz FreeSurfer-BET: T1w_brain_template_mask_ccs: /ccs_template/MNI152_T1_1mm_first_brain_mask.nii.gz