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shnizzedyshnizzedy
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fixup! ⏩ Bring develop up to date with main 
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‎CPAC/resources/configs/pipeline_config_blank.yml‎

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@@ -1214,10 +1214,10 @@ timeseries_extraction:
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/ndmg_atlases/label/Human/HarvardOxfordsub-maxprob-thr25_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/Juelich_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/MICCAI_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/Schaefer1000_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/Schaefer200_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/Schaefer300_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/Schaefer400_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-1000Parcels17NetworksOrder.nii.gz: Avg
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/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-200Parcels17NetworksOrder.nii.gz: Avg
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/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-300Parcels17NetworksOrder.nii.gz: Avg
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/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-400Parcels17NetworksOrder.nii.gz: Avg
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/ndmg_atlases/label/Human/Talairach_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/Brodmann_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/Desikan_space-MNI152NLin6_res-1x1x1.nii.gz: Avg

‎CPAC/resources/configs/pipeline_config_fmriprep-options.yml‎

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@@ -293,11 +293,11 @@ registration_workflows:
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apply_transform:
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# options: 'default', 'abcd', 'single_step_resampling'
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# options: 'default', 'abcd', 'single_step_resampling_from_stc'
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# 'default': apply func-to-anat and anat-to-template transforms on motion corrected functional image.
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# 'abcd': apply motion correction, func-to-anat and anat-to-template transforms on each of raw functional volume using FSL applywarp based on ABCD-HCP pipeline.
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# 'single_step_resampling': apply motion correction, func-to-anat and anat-to-template transforms on each of raw functional volume using ANTs antsApplyTransform based on fMRIPrep pipeline.
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using: 'single_step_resampling'
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# 'single_step_resampling_from_stc': apply motion correction, func-to-anat and anat-to-template transforms on each of raw functional volume using ANTs antsApplyTransform based on fMRIPrep pipeline.
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using: 'single_step_resampling_from_stc'
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functional_preproc:
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motion_estimates_and_correction:
@@ -339,6 +339,9 @@ nuisance_corrections:
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# run: [On, Off] - this will run both and fork the pipeline
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run: [Off]
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# run nuisance regression in BOLD or template space
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space: template
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# switch to Off if nuisance regression is off and you don't want to write out the regressors
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create_regressors: On
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‎CPAC/resources/configs/pipeline_config_monkey-ABCD.yml‎

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@@ -322,10 +322,10 @@ registration_workflows:
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apply_transform:
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# options: 'default', 'abcd', 'single_step_resampling', 'dcan_nhp'
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# options: 'default', 'abcd', 'single_step_resampling_from_stc', 'dcan_nhp'
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# 'default': apply func-to-anat and anat-to-template transforms on motion corrected functional image.
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# 'abcd': apply motion correction, func-to-anat and anat-to-template transforms on each of raw functional volume using FSL applywarp based on ABCD-HCP pipeline.
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# 'single_step_resampling': apply motion correction, func-to-anat and anat-to-template transforms on each of raw functional volume using ANTs antsApplyTransform based on fMRIPrep pipeline.
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# 'single_step_resampling_from_stc': apply motion correction, func-to-anat and anat-to-template transforms on each of raw functional volume using ANTs antsApplyTransform based on fMRIPrep pipeline.
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using: 'dcan_nhp'
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functional_preproc:

‎CPAC/resources/configs/pipeline_config_rbc-options.yml‎

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@@ -113,30 +113,7 @@ functional_preproc:
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nuisance_corrections:
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2-nuisance_regression:
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Regressors:
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- Name: Motion-regressor-no-GSR-or-aCompCor
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Bandpass:
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bottom_frequency: 0.01
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top_frequency: 0.1
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CerebrospinalFluid:
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erode_mask: false
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extraction_resolution: 2
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include_delayed: true
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include_delayed_squared: true
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include_squared: true
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summary: Mean
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Motion:
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include_delayed: true
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include_delayed_squared: true
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include_squared: true
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WhiteMatter:
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erode_mask: false
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extraction_resolution: 2
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include_delayed: true
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include_delayed_squared: true
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include_squared: true
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summary: Mean
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- Name: Regressor-with-GSR
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- Name: 36-parameter
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Bandpass:
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bottom_frequency: 0.01
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top_frequency: 0.1
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include_squared: true
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summary: Mean
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- Name: Regressor-with-aCompCor
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- Name: aCompCor
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Bandpass:
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bottom_frequency: 0.01
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top_frequency: 0.1
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- Partial
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tse_roi_paths:
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# AAL
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/ndmg_atlases/label/Human/AAL_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/AAL_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
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# Atlases
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/ndmg_atlases/label/Human/Brodmann_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/Glasser_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/Brodmann_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
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/ndmg_atlases/label/Human/Glasser_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
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# Slab
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/ndmg_atlases/label/Human/Slab907_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/Slab907_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
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# HO: Thresholded
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/ndmg_atlases/label/Human/HarvardOxfordcort-maxprob-thr25_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/HarvardOxfordsub-maxprob-thr25_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/HarvardOxfordcort-maxprob-thr25_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
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/ndmg_atlases/label/Human/HarvardOxfordsub-maxprob-thr25_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
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# Jeulich
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/ndmg_atlases/label/Human/Juelich_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/Juelich_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
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# CC
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/cpac_templates/CC200.nii.gz: Avg
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/cpac_templates/CC400.nii.gz: Avg
@@ -241,10 +218,10 @@ timeseries_extraction:
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/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-1000Parcels17NetworksOrder.nii.gz: Avg
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# Networks
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# Yeo
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/ndmg_atlases/label/Human/Yeo-17-liberal_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/Yeo-17_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/Yeo-7-liberal_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/Yeo-7_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
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/ndmg_atlases/label/Human/Yeo-17-liberal_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
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/ndmg_atlases/label/Human/Yeo-17_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
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/ndmg_atlases/label/Human/Yeo-7-liberal_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
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/ndmg_atlases/label/Human/Yeo-7_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
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# Smith 2009 (to be included after https://github.com/FCP-INDI/C-PAC/issues/1640 is resolved)
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# /cpac_templates/Smith_space-MNI152NLin6_res-3x3x3_desc-thresh3_mask.nii.gz: Avg
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