⏩ Bring develop up to date with main

Author: shnizzedy

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
-    /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/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
     /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

CPAC/resources/configs/pipeline_config_fmriprep-options.yml

@@ -293,11 +293,11 @@ registration_workflows:
 
       apply_transform:
 
-        # options: 'default', 'abcd', 'single_step_resampling_from_stc'
+        # options: 'default', 'abcd', 'single_step_resampling'
         # '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_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'
+        # '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'
 
 functional_preproc: 
   motion_estimates_and_correction: 
@@ -339,9 +339,6 @@ 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
 

CPAC/resources/configs/pipeline_config_monkey-ABCD.yml

@@ -322,10 +322,10 @@ registration_workflows:
 
       apply_transform:
 
-        # options: 'default', 'abcd', 'single_step_resampling_from_stc', 'dcan_nhp'
+        # options: 'default', 'abcd', 'single_step_resampling', '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_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.
+        # '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: 'dcan_nhp'
 
 functional_preproc:

CPAC/resources/configs/pipeline_config_rbc-options.yml

@@ -113,7 +113,30 @@ functional_preproc:
 nuisance_corrections:
   2-nuisance_regression:
     Regressors:
-      - Name: 36-parameter
+      - 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
         Bandpass:
           bottom_frequency: 0.01
           top_frequency: 0.1
@@ -141,7 +164,7 @@ nuisance_corrections:
           include_squared: true
           summary: Mean
 
-      - Name: aCompCor
+      - Name: Regressor-with-aCompCor
         Bandpass:
           bottom_frequency: 0.01
           top_frequency: 0.1
@@ -197,17 +220,17 @@ timeseries_extraction:
       - Partial
   tse_roi_paths:
     # AAL
-    /ndmg_atlases/label/Human/AAL_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
+    /ndmg_atlases/label/Human/AAL_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
     # Atlases
-    /ndmg_atlases/label/Human/Brodmann_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
-    /ndmg_atlases/label/Human/Glasser_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
+    /ndmg_atlases/label/Human/Brodmann_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
+    /ndmg_atlases/label/Human/Glasser_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
     # Slab
-    /ndmg_atlases/label/Human/Slab907_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
+    /ndmg_atlases/label/Human/Slab907_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
     # HO: Thresholded
-    /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
+    /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
     # Jeulich
-    /ndmg_atlases/label/Human/Juelich_space-MNI152NLin6_res-2x2x2.nii.gz: Avg
+    /ndmg_atlases/label/Human/Juelich_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
     # CC
     /cpac_templates/CC200.nii.gz: Avg
     /cpac_templates/CC400.nii.gz: Avg
@@ -218,10 +241,10 @@ 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-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
+    /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
     #  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
 

README.md

@@ -40,7 +40,7 @@ Documentation pertaining to this latest release can be found here: https://fcp-i
 Discussion Forum
 ---------------
 
-If you are stuck and need help or have any other questions or comments about C-PAC, there is a C-PAC discussion forum here: ttps://neurostars.org/tag/cpac
+If you are stuck and need help or have any other questions or comments about C-PAC, there is a C-PAC discussion forum here: https://neurostars.org/tag/cpac
 
 Issue Tracker and Bugs
 ----------------------