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💡 Update comments based on default preconfig
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‎CPAC/resources/configs/pipeline_config_abcd-options.yml‎

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@@ -37,6 +37,9 @@ surface_analysis:
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# select those 'Freesurfer-' labeled options further below in anatomical_preproc.
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freesurfer:
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# Ingress freesurfer recon-all folder
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ingress_reconall: Off
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# FreeSurfer will run as part of configured brain extraction in this specific configuration, so FreeSurfer's independent run was automatically disabled.
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run_reconall: Off
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‎CPAC/resources/configs/pipeline_config_anat-only.yml‎

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# Sparsity value for Sparsity Threshold
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# Pearson's r value for Correlation Threshold
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correlation_threshold: 0.001
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# PREPROCESSING
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# -------------
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surface_analysis:
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# Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
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# If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
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# select those 'Freesurfer-' labeled options further below in anatomical_preproc.
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freesurfer:
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# Ingress freesurfer recon-all folder
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ingress_reconall: Off

‎CPAC/resources/configs/pipeline_config_benchmark-ANTS.yml‎

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# /path/to/atlas.nii.gz: Avg, DualReg, MultReg
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sca_roi_paths:
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s3://fcp-indi/resources/cpac/resources/rois_2mm.nii.gz: Avg, MultReg
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# PREPROCESSING
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# -------------
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surface_analysis:
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# Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
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# If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
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# select those 'Freesurfer-' labeled options further below in anatomical_preproc.
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freesurfer:
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# Ingress freesurfer recon-all folder
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ingress_reconall: Off

‎CPAC/resources/configs/pipeline_config_benchmark-FNIRT.yml‎

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# /path/to/atlas.nii.gz: Avg, DualReg, MultReg
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sca_roi_paths:
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s3://fcp-indi/resources/cpac/resources/rois_2mm.nii.gz: Avg, MultReg
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# PREPROCESSING
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# -------------
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surface_analysis:
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# Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
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# If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
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# select those 'Freesurfer-' labeled options further below in anatomical_preproc.
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freesurfer:
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# Ingress freesurfer recon-all folder
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ingress_reconall: Off

‎CPAC/resources/configs/pipeline_config_ccs-options.yml‎

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# Add extra arguments to recon-all command
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reconall_args: -clean-bm -gcut
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# Ingress freesurfer recon-all folder
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ingress_reconall: Off
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anatomical_preproc:
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run: On
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acpc_alignment:

‎CPAC/resources/configs/pipeline_config_default-deprecated.yml‎

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# Calculate Degree, Eigenvector Centrality, or Functional Connectivity Density.
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run: On
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# PREPROCESSING
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# -------------
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surface_analysis:
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# Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
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# If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
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# select those 'Freesurfer-' labeled options further below in anatomical_preproc.
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freesurfer:
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# Ingress freesurfer recon-all folder
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ingress_reconall: Off

‎CPAC/resources/configs/pipeline_config_fmriprep-options.yml‎

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# Template-space eye mask
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eye_mask_path:
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# PREPROCESSING
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# -------------
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surface_analysis:
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# Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
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# If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
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# select those 'Freesurfer-' labeled options further below in anatomical_preproc.
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freesurfer:
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# Ingress freesurfer recon-all folder
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ingress_reconall: Off

‎CPAC/resources/configs/pipeline_config_fx-options.yml‎

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summary: Mean
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PolyOrt:
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degree: 2
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# PREPROCESSING
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# -------------
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surface_analysis:
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# Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
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# If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
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# select those 'Freesurfer-' labeled options further below in anatomical_preproc.
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freesurfer:
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# Ingress freesurfer recon-all folder
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ingress_reconall: Off

‎CPAC/resources/configs/pipeline_config_monkey-ABCD.yml‎

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/Template/DMN-Ghahremani2016/thr_bin_hjin/HRzstat_DMN_3_thr4.nii.gz: Avg
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s3://fcp-indi/resources/cpac/resources/parcellation/Markov91_L_0.5mm.nii.gz: Avg
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s3://fcp-indi/resources/cpac/resources/parcellation/Markov91_R_0.5mm.nii.gz: Avg
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# PREPROCESSING
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# -------------
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surface_analysis:
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# Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
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# If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
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# select those 'Freesurfer-' labeled options further below in anatomical_preproc.
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freesurfer:
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# Ingress freesurfer recon-all folder
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ingress_reconall: Off

‎CPAC/resources/configs/pipeline_config_monkey.yml‎

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sca_roi_paths:
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s3://fcp-indi/resources/cpac/resources/parcellation/Markov91_L_0.5mm.nii.gz: Avg
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s3://fcp-indi/resources/cpac/resources/parcellation/Markov91_R_0.5mm.nii.gz: Avg
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# PREPROCESSING
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# -------------
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surface_analysis:
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# Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
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# If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
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# select those 'Freesurfer-' labeled options further below in anatomical_preproc.
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freesurfer:
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# Ingress freesurfer recon-all folder
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ingress_reconall: Off

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