📦️ Get MacaqueYerkes19 & J_Macaque_11mo_atlas_nACQ from DCAN repo (#1619)

Author: shnizzedy

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - `master` branch renamed `main`
+- Packaged templates in https://github.com/FCP-INDI/C-PAC_templates
 
 ### Deprecated
 

CPAC/resources/configs/pipeline_config_blank.yml

@@ -458,8 +458,8 @@ segmentation:
 
       # The atlas image assumed to be used in ANTs Prior-based Segmentation.
       template_brain_list :
-        - /monkey_seg/templates/JointLabelCouncil/MacaqueYerkes19_T1w_0.5mm/T1w_brain.nii.gz
-        - /monkey_seg/templates/JointLabelCouncil/J_Macaque_11mo_atlas_nACQ_194x252x160space_0.5mm/T1w_brain.nii.gz
+        - /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
 
       # The atlas segmentation images.
       # For performing ANTs Prior-based segmentation method
@@ -472,8 +472,8 @@ segmentation:
       #   - segmentation1.nii.gz
       #   - segmentation1.nii.gz
       template_segmentation_list:
-        - /monkey_seg/templates/JointLabelCouncil/MacaqueYerkes19_T1w_0.5mm/Segmentation.nii.gz
-        - /monkey_seg/templates/JointLabelCouncil/J_Macaque_11mo_atlas_nACQ_194x252x160space_0.5mm/Segmentation.nii.gz
+        - /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
 
       # Label values corresponding to CSF/GM/WM in atlas file
       # It is not necessary to change this values unless your CSF/GM/WM label values are different from Freesurfer Color Lookup Table.

CPAC/resources/configs/pipeline_config_monkey-ABCD.yml

@@ -110,10 +110,10 @@ anatomical_preproc:
     acpc_target: 'brain'
 
     # ACPC aligned template
-    T1w_ACPC_template: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1w_0.5mm.nii.gz
-    T1w_brain_ACPC_template: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1w_0.5mm_brain.nii.gz
-    T2w_ACPC_template: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T2w_0.5mm.nii.gz
-    T2w_brain_ACPC_template: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T2w_0.5mm_brain.nii.gz
+    T1w_ACPC_template: /cpac_templates/MacaqueYerkes19_T1w_0.5mm.nii.gz
+    T1w_brain_ACPC_template: /cpac_templates/MacaqueYerkes19_T1w_0.5mm_brain.nii.gz
+    T2w_ACPC_template: /cpac_templates/MacaqueYerkes19_T2w_0.5mm.nii.gz
+    T2w_brain_ACPC_template: /cpac_templates/MacaqueYerkes19_T2w_0.5mm_brain.nii.gz
 
   brain_extraction: 
 
@@ -227,15 +227,15 @@ registration_workflows:
 
     # Template to be used during registration.
     # It is not necessary to change this path unless you intend to use a non-standard template.
-    T1w_brain_template: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1w_0.5mm_brain.nii.gz
+    T1w_brain_template: /cpac_templates/MacaqueYerkes19_T1w_0.5mm_brain.nii.gz
 
     # Template to be used during registration.
     # It is not necessary to change this path unless you intend to use a non-standard template.
-    T1w_template: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1w_0.5mm.nii.gz
+    T1w_template: /cpac_templates/MacaqueYerkes19_T1w_0.5mm.nii.gz
 
     # Template to be used during registration.
     # It is not necessary to change this path unless you intend to use a non-standard template.
-    T1w_brain_template_mask: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1w_0.5mm_brain_mask.nii.gz
+    T1w_brain_template_mask: /cpac_templates/MacaqueYerkes19_T1w_0.5mm_brain_mask.nii.gz
 
     # Register skull-on anatomical image to a template.
     reg_with_skull: Off
@@ -255,15 +255,15 @@ registration_workflows:
         ref_resolution: 1mm
 
         # Reference mask for FSL registration.
-        ref_mask: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1w_1.0mm_brain_mask.nii.gz
+        ref_mask: /cpac_templates/MacaqueYerkes19_T1w_1.0mm_brain_mask.nii.gz
 
         # Template to be used during registration.
         # It is not necessary to change this path unless you intend to use a non-standard template.
-        FNIRT_T1w_brain_template: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1w_1.0mm_brain.nii.gz
+        FNIRT_T1w_brain_template: /cpac_templates/MacaqueYerkes19_T1w_1.0mm_brain.nii.gz
 
         # Template to be used during registration.
         # It is not necessary to change this path unless you intend to use a non-standard template.
-        FNIRT_T1w_template: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1w_1.0mm.nii.gz
+        FNIRT_T1w_template: /cpac_templates/MacaqueYerkes19_T1w_1.0mm.nii.gz
 
         # Interpolation method for writing out transformed anatomical images.
         # Possible values: trilinear, sinc, spline
@@ -353,18 +353,18 @@ registration_workflows:
 
           # Standard Skull Stripped Template. Used as a reference image for functional registration.
           # This can be different than the template used as the reference/fixed for T1-to-template registration.
-          T1w_brain_template_funcreg: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1w_1.5mm_brain.nii.gz
+          T1w_brain_template_funcreg: /cpac_templates/MacaqueYerkes19_T1w_1.5mm_brain.nii.gz
 
           # Standard Anatomical Brain Image with Skull.
           # This can be different than the template used as the reference/fixed for T1-to-template registration.
-          T1w_template_funcreg: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1_0.5mm.nii.gz
+          T1w_template_funcreg: /cpac_templates/MacaqueYerkes19_T1_0.5mm.nii.gz
 
           # Template to be used during registration.
           # It is not necessary to change this path unless you intend to use a non-standard template.
-          T1w_brain_template_mask_funcreg: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1w_1.5mm_brain_mask.nii.gz
+          T1w_brain_template_mask_funcreg: /cpac_templates/MacaqueYerkes19_T1w_1.5mm_brain_mask.nii.gz
 
           # a standard template for resampling if using float resolution
-          T1w_template_for_resample:  /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1w_0.5mm.nii.gz
+          T1w_template_for_resample:  /cpac_templates/MacaqueYerkes19_T1w_0.5mm.nii.gz
 
       FNIRT_pipelines:
 
@@ -555,24 +555,24 @@ voxel_mirrored_homotopic_connectivity:
 
     # Included as part of the 'Image Resource Files' package available on the Install page of the User Guide.
     # It is not necessary to change this path unless you intend to use a non-standard symmetric template.
-    T1w_brain_template_symmetric: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1w_1.0mm_brain.nii.gz
+    T1w_brain_template_symmetric: /cpac_templates/MacaqueYerkes19_T1w_1.0mm_brain.nii.gz
 
     # A reference symmetric brain template for resampling
-    T1w_brain_template_symmetric_for_resample: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1w_1.0mm.nii.gz
+    T1w_brain_template_symmetric_for_resample: /cpac_templates/MacaqueYerkes19_T1w_1.0mm.nii.gz
 
     # Included as part of the 'Image Resource Files' package available on the Install page of the User Guide.
     # It is not necessary to change this path unless you intend to use a non-standard symmetric template.
-    T1w_template_symmetric: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1w_1.0mm.nii.gz
+    T1w_template_symmetric: /cpac_templates/MacaqueYerkes19_T1w_1.0mm.nii.gz
 
     # A reference symmetric skull template for resampling
-    T1w_template_symmetric_for_resample: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1w_1.0mm.nii.gz
+    T1w_template_symmetric_for_resample: /cpac_templates/MacaqueYerkes19_T1w_1.0mm.nii.gz
 
     # Included as part of the 'Image Resource Files' package available on the Install page of the User Guide.
     # It is not necessary to change this path unless you intend to use a non-standard symmetric template.
-    dilated_symmetric_brain_mask: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1w_2mm_brain_mask.nii.gz
+    dilated_symmetric_brain_mask: /cpac_templates/MacaqueYerkes19_T1w_2mm_brain_mask.nii.gz
 
     # A reference symmetric brain mask template for resampling
-    dilated_symmetric_brain_mask_for_resample: /DCAN_MacaqueYerkes19_template/MacaqueYerkes19_T1w_2mm_brain_mask.nii.gz
+    dilated_symmetric_brain_mask_for_resample: /cpac_templates/MacaqueYerkes19_T1w_2mm_brain_mask.nii.gz
 
 network_centrality: 
 

CPAC/resources/configs/pipeline_config_monkey.yml

@@ -100,10 +100,10 @@ anatomical_preproc:
     FOV_crop: flirt
 
     # ACPC aligned template
-    T1w_ACPC_template: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_0.5mm.nii.gz
-    T1w_brain_ACPC_template: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_0.5mm_brain.nii.gz
-    T2w_ACPC_template: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T2w_0.5mm.nii.gz
-    T2w_brain_ACPC_template: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T2w_0.5mm_brain.nii.gz
+    T1w_ACPC_template: /cpac_templates/MacaqueYerkes19_T1w_0.5mm.nii.gz
+    T1w_brain_ACPC_template: /cpac_templates/MacaqueYerkes19_T1w_0.5mm_brain.nii.gz
+    T2w_ACPC_template: /cpac_templates/MacaqueYerkes19_T2w_0.5mm.nii.gz
+    T2w_brain_ACPC_template: /cpac_templates/MacaqueYerkes19_T2w_0.5mm_brain.nii.gz
 
   brain_extraction: 
 
@@ -195,11 +195,11 @@ registration_workflows:
 
     # Template to be used during registration.
     # It is not necessary to change this path unless you intend to use a non-standard template.
-    T1w_brain_template: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_1.0mm_brain.nii.gz
+    T1w_brain_template: /cpac_templates/MacaqueYerkes19_T1w_1.0mm_brain.nii.gz
 
     # Template to be used during registration.
     # It is not necessary to change this path unless you intend to use a non-standard template.
-    T1w_template: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_1.0mm.nii.gz
+    T1w_template: /cpac_templates/MacaqueYerkes19_T1w_1.0mm.nii.gz
 
     # Register skull-on anatomical image to a template.
     reg_with_skull: Off
@@ -209,7 +209,7 @@ registration_workflows:
       FSL-FNIRT: 
 
         # Reference mask for FSL registration.
-        ref_mask: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_1.0mm_brain_mask.nii.gz
+        ref_mask: /cpac_templates/MacaqueYerkes19_T1w_1.0mm_brain_mask.nii.gz
 
   functional_registration: 
 
@@ -278,11 +278,11 @@ registration_workflows:
 
           # Standard Skull Stripped Template. Used as a reference image for functional registration.
           # This can be different than the template used as the reference/fixed for T1-to-template registration.
-          T1w_brain_template_funcreg: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_2mm_brain.nii.gz
+          T1w_brain_template_funcreg: /cpac_templates/MacaqueYerkes19_T1w_2mm_brain.nii.gz
 
           # Standard Anatomical Brain Image with Skull.
           # This can be different than the template used as the reference/fixed for T1-to-template registration.
-          T1w_template_funcreg: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_2mm.nii.gz
+          T1w_template_funcreg: /cpac_templates/MacaqueYerkes19_T1w_2mm.nii.gz
 
 functional_preproc: 
 
@@ -389,24 +389,24 @@ voxel_mirrored_homotopic_connectivity:
 
     # Included as part of the 'Image Resource Files' package available on the Install page of the User Guide.
     # It is not necessary to change this path unless you intend to use a non-standard symmetric template.
-    T1w_brain_template_symmetric: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_1.0mm_brain.nii.gz
+    T1w_brain_template_symmetric: /cpac_templates/MacaqueYerkes19_T1w_1.0mm_brain.nii.gz
 
     # A reference symmetric brain template for resampling
-    T1w_brain_template_symmetric_for_resample: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_1.0mm.nii.gz
+    T1w_brain_template_symmetric_for_resample: /cpac_templates/resources/MacaqueYerkes19_T1w_1.0mm.nii.gz
 
     # Included as part of the 'Image Resource Files' package available on the Install page of the User Guide.
     # It is not necessary to change this path unless you intend to use a non-standard symmetric template.
-    T1w_template_symmetric: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_1.0mm.nii.gz
+    T1w_template_symmetric: /cpac_templates/MacaqueYerkes19_T1w_1.0mm.nii.gz
 
     # A reference symmetric skull template for resampling
-    T1w_template_symmetric_for_resample: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_1.0mm.nii.gz
+    T1w_template_symmetric_for_resample: /cpac_templates/MacaqueYerkes19_T1w_1.0mm.nii.gz
 
     # Included as part of the 'Image Resource Files' package available on the Install page of the User Guide.
     # It is not necessary to change this path unless you intend to use a non-standard symmetric template.
-    dilated_symmetric_brain_mask: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_2mm_brain_mask.nii.gz
+    dilated_symmetric_brain_mask: /cpac_templates/MacaqueYerkes19_T1w_2mm_brain_mask.nii.gz
 
     # A reference symmetric brain mask template for resampling
-    dilated_symmetric_brain_mask_for_resample: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_2mm_brain_mask.nii.gz
+    dilated_symmetric_brain_mask_for_resample: /cpac_templates/MacaqueYerkes19_T1w_2mm_brain_mask.nii.gz
 
 network_centrality: 
 

CPAC/resources/configs/pipeline_config_nhp-macaque.yml

@@ -95,7 +95,7 @@ anatomical_preproc:
     brain_size: 70
 
     # ACPC aligned template
-    T1w_ACPC_template: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_0.5mm.nii.gz
+    T1w_ACPC_template: /cpac_templates/MacaqueYerkes19_T1w_0.5mm.nii.gz
 
   brain_extraction: 
 
@@ -185,11 +185,11 @@ registration_workflows:
 
     # Template to be used during registration.
     # It is not necessary to change this path unless you intend to use a non-standard template.
-    T1w_brain_template: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_1.0mm_brain.nii.gz
+    T1w_brain_template: /cpac_templates/MacaqueYerkes19_T1w_1.0mm_brain.nii.gz
 
     # Template to be used during registration.
     # It is not necessary to change this path unless you intend to use a non-standard template.
-    T1w_template: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_1.0mm.nii.gz
+    T1w_template: /cpac_templates/MacaqueYerkes19_T1w_1.0mm.nii.gz
 
     # Register skull-on anatomical image to a template.
     reg_with_skull: Off
@@ -199,7 +199,7 @@ registration_workflows:
       FSL-FNIRT: 
 
         # Reference mask for FSL registration.
-        ref_mask: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_1.0mm_brain_mask.nii.gz
+        ref_mask: /cpac_templates/MacaqueYerkes19_T1w_1.0mm_brain_mask.nii.gz
 
   functional_registration: 
 
@@ -259,11 +259,11 @@ registration_workflows:
 
           # Standard Skull Stripped Template. Used as a reference image for functional registration.
           # This can be different than the template used as the reference/fixed for T1-to-template registration.
-          T1w_brain_template_funcreg: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_2mm_brain.nii.gz
+          T1w_brain_template_funcreg: /cpac_templates/MacaqueYerkes19_T1w_2mm_brain.nii.gz
 
           # Standard Anatomical Brain Image with Skull.
           # This can be different than the template used as the reference/fixed for T1-to-template registration.
-          T1w_template_funcreg: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_2mm.nii.gz
+          T1w_template_funcreg: /cpac_templates/MacaqueYerkes19_T1w_2mm.nii.gz
 
 functional_preproc: 
 
@@ -370,24 +370,24 @@ voxel_mirrored_homotopic_connectivity:
 
     # Included as part of the 'Image Resource Files' package available on the Install page of the User Guide.
     # It is not necessary to change this path unless you intend to use a non-standard symmetric template.
-    T1w_brain_template_symmetric: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_1.0mm_brain.nii.gz
+    T1w_brain_template_symmetric: /cpac_templates/MacaqueYerkes19_T1w_1.0mm_brain.nii.gz
 
     # A reference symmetric brain template for resampling
-    T1w_brain_template_symmetric_for_resample: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_1.0mm.nii.gz
+    T1w_brain_template_symmetric_for_resample: /cpac_templates/MacaqueYerkes19_T1w_1.0mm.nii.gz
 
     # Included as part of the 'Image Resource Files' package available on the Install page of the User Guide.
     # It is not necessary to change this path unless you intend to use a non-standard symmetric template.
-    T1w_template_symmetric: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_1.0mm.nii.gz
+    T1w_template_symmetric: /cpac_templates/MacaqueYerkes19_T1w_1.0mm.nii.gz
 
     # A reference symmetric skull template for resampling
-    T1w_template_symmetric_for_resample: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_1.0mm.nii.gz
+    T1w_template_symmetric_for_resample: /cpac_templates/MacaqueYerkes19_T1w_1.0mm.nii.gz
 
     # Included as part of the 'Image Resource Files' package available on the Install page of the User Guide.
     # It is not necessary to change this path unless you intend to use a non-standard symmetric template.
-    dilated_symmetric_brain_mask: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_2mm_brain_mask.nii.gz
+    dilated_symmetric_brain_mask: /cpac_templates/MacaqueYerkes19_T1w_2mm_brain_mask.nii.gz
 
     # A reference symmetric brain mask template for resampling
-    dilated_symmetric_brain_mask_for_resample: s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_2mm_brain_mask.nii.gz
+    dilated_symmetric_brain_mask_for_resample: /cpac_templates/MacaqueYerkes19_T1w_2mm_brain_mask.nii.gz
 
 network_centrality: 
 

dev/docker_data/default_pipeline.yml

@@ -510,8 +510,8 @@ segmentation:
 
       # The atlas image assumed to be used in ANTs Prior-based Segmentation.
       template_brain_list :
-        - /monkey_seg/templates/JointLabelCouncil/MacaqueYerkes19_T1w_0.5mm/T1w_brain.nii.gz
-        - /monkey_seg/templates/JointLabelCouncil/J_Macaque_11mo_atlas_nACQ_194x252x160space_0.5mm/T1w_brain.nii.gz
+        - /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
 
       # The atlas segmentation images.
       # For performing ANTs Prior-based segmentation method
@@ -524,8 +524,8 @@ segmentation:
       #   - segmentation1.nii.gz
       #   - segmentation1.nii.gz
       template_segmentation_list:
-        - /monkey_seg/templates/JointLabelCouncil/MacaqueYerkes19_T1w_0.5mm/Segmentation.nii.gz
-        - /monkey_seg/templates/JointLabelCouncil/J_Macaque_11mo_atlas_nACQ_194x252x160space_0.5mm/Segmentation.nii.gz
+        - /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
 
       # Label values corresponding to CSF/GM/WM in atlas file
       # It is not necessary to change this values unless your CSF/GM/WM label values are different from Freesurfer Color Lookup Table.