diff --git a/CPAC/resources/configs/pipeline_config_blank.yml b/CPAC/resources/configs/pipeline_config_blank.yml index 9b948f42fe..1b47e0681a 100644 --- a/CPAC/resources/configs/pipeline_config_blank.yml +++ b/CPAC/resources/configs/pipeline_config_blank.yml @@ -1214,10 +1214,10 @@ timeseries_extraction: /ndmg_atlases/label/Human/HarvardOxfordsub-maxprob-thr25_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Juelich_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/MICCAI_space-MNI152NLin6_res-1x1x1.nii.gz: Avg - /ndmg_atlases/label/Human/Schaefer1000_space-MNI152NLin6_res-1x1x1.nii.gz: Avg - /ndmg_atlases/label/Human/Schaefer200_space-MNI152NLin6_res-1x1x1.nii.gz: Avg - /ndmg_atlases/label/Human/Schaefer300_space-MNI152NLin6_res-1x1x1.nii.gz: Avg - /ndmg_atlases/label/Human/Schaefer400_space-MNI152NLin6_res-1x1x1.nii.gz: Avg + /cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-1000Parcels17NetworksOrder.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 /ndmg_atlases/label/Human/Talairach_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Brodmann_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Desikan_space-MNI152NLin6_res-1x1x1.nii.gz: Avg diff --git a/CPAC/resources/configs/pipeline_config_fmriprep-options.yml b/CPAC/resources/configs/pipeline_config_fmriprep-options.yml index 447d5fdaa5..ddf1a088da 100644 --- a/CPAC/resources/configs/pipeline_config_fmriprep-options.yml +++ b/CPAC/resources/configs/pipeline_config_fmriprep-options.yml @@ -293,11 +293,11 @@ registration_workflows: apply_transform: - # options: 'default', 'abcd', 'single_step_resampling' + # options: 'default', 'abcd', 'single_step_resampling_from_stc' # 'default': apply func-to-anat and anat-to-template transforms on motion corrected functional image. # '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. - # '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. - using: 'single_step_resampling' + # '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. + using: 'single_step_resampling_from_stc' functional_preproc: motion_estimates_and_correction: @@ -339,6 +339,9 @@ nuisance_corrections: # run: [On, Off] - this will run both and fork the pipeline run: [Off] + # run nuisance regression in BOLD or template space + space: template + # switch to Off if nuisance regression is off and you don't want to write out the regressors create_regressors: On diff --git a/CPAC/resources/configs/pipeline_config_monkey-ABCD.yml b/CPAC/resources/configs/pipeline_config_monkey-ABCD.yml index 35f380877f..97408657af 100644 --- a/CPAC/resources/configs/pipeline_config_monkey-ABCD.yml +++ b/CPAC/resources/configs/pipeline_config_monkey-ABCD.yml @@ -322,10 +322,10 @@ registration_workflows: apply_transform: - # options: 'default', 'abcd', 'single_step_resampling', 'dcan_nhp' + # options: 'default', 'abcd', 'single_step_resampling_from_stc', 'dcan_nhp' # 'default': apply func-to-anat and anat-to-template transforms on motion corrected functional image. # '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. - # '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. + # '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. using: 'dcan_nhp' functional_preproc: diff --git a/CPAC/resources/configs/pipeline_config_rbc-options.yml b/CPAC/resources/configs/pipeline_config_rbc-options.yml index 13f9475277..b8950b759c 100644 --- a/CPAC/resources/configs/pipeline_config_rbc-options.yml +++ b/CPAC/resources/configs/pipeline_config_rbc-options.yml @@ -113,30 +113,7 @@ functional_preproc: nuisance_corrections: 2-nuisance_regression: Regressors: - - Name: Motion-regressor-no-GSR-or-aCompCor - Bandpass: - bottom_frequency: 0.01 - top_frequency: 0.1 - CerebrospinalFluid: - erode_mask: false - extraction_resolution: 2 - include_delayed: true - include_delayed_squared: true - include_squared: true - summary: Mean - Motion: - include_delayed: true - include_delayed_squared: true - include_squared: true - WhiteMatter: - erode_mask: false - extraction_resolution: 2 - include_delayed: true - include_delayed_squared: true - include_squared: true - summary: Mean - - - Name: Regressor-with-GSR + - Name: 36-parameter Bandpass: bottom_frequency: 0.01 top_frequency: 0.1 @@ -164,7 +141,7 @@ nuisance_corrections: include_squared: true summary: Mean - - Name: Regressor-with-aCompCor + - Name: aCompCor Bandpass: bottom_frequency: 0.01 top_frequency: 0.1 @@ -220,17 +197,17 @@ timeseries_extraction: - Partial tse_roi_paths: # AAL - /ndmg_atlases/label/Human/AAL_space-MNI152NLin6_res-1x1x1.nii.gz: Avg + /ndmg_atlases/label/Human/AAL_space-MNI152NLin6_res-2x2x2.nii.gz: Avg # Atlases - /ndmg_atlases/label/Human/Brodmann_space-MNI152NLin6_res-1x1x1.nii.gz: Avg - /ndmg_atlases/label/Human/Glasser_space-MNI152NLin6_res-1x1x1.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 # Slab - /ndmg_atlases/label/Human/Slab907_space-MNI152NLin6_res-1x1x1.nii.gz: Avg + /ndmg_atlases/label/Human/Slab907_space-MNI152NLin6_res-2x2x2.nii.gz: Avg # HO: Thresholded - /ndmg_atlases/label/Human/HarvardOxfordcort-maxprob-thr25_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/HarvardOxfordcort-maxprob-thr25_space-MNI152NLin6_res-2x2x2.nii.gz: Avg + /ndmg_atlases/label/Human/HarvardOxfordsub-maxprob-thr25_space-MNI152NLin6_res-2x2x2.nii.gz: Avg # Jeulich - /ndmg_atlases/label/Human/Juelich_space-MNI152NLin6_res-1x1x1.nii.gz: Avg + /ndmg_atlases/label/Human/Juelich_space-MNI152NLin6_res-2x2x2.nii.gz: Avg # CC /cpac_templates/CC200.nii.gz: Avg /cpac_templates/CC400.nii.gz: Avg @@ -241,10 +218,10 @@ timeseries_extraction: /cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-1000Parcels17NetworksOrder.nii.gz: Avg # Networks # Yeo - /ndmg_atlases/label/Human/Yeo-17-liberal_space-MNI152NLin6_res-1x1x1.nii.gz: Avg - /ndmg_atlases/label/Human/Yeo-17_space-MNI152NLin6_res-1x1x1.nii.gz: Avg - /ndmg_atlases/label/Human/Yeo-7-liberal_space-MNI152NLin6_res-1x1x1.nii.gz: Avg - /ndmg_atlases/label/Human/Yeo-7_space-MNI152NLin6_res-1x1x1.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 # Smith 2009 (to be included after https://github.com/FCP-INDI/C-PAC/issues/1640 is resolved) # /cpac_templates/Smith_space-MNI152NLin6_res-3x3x3_desc-thresh3_mask.nii.gz: Avg