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🚚 ref_mask_res-2 and T1w_template_res-2 fields are moved out of registration and into surface.
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‎CHANGELOG.md‎

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@@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- Moved `pygraphviz` from requirements to `graphviz` optional dependencies group.
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- Automatically tag untagged `subject_id` and `unique_id` as `!!str` when loading data config files.
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- Made orientation configurable (was hard-coded as "RPI").
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- Moved `ref_mask_res_2` and `T1w_template_res-2` fields from registration into surface under `abcd_prefreesurfer_prep`.
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### Fixed
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‎CPAC/pipeline/schema.py‎

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@@ -712,8 +712,6 @@ def sanitize(filename):
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"interpolation": In({"trilinear", "sinc", "spline"}),
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"identity_matrix": Maybe(str),
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"ref_mask": Maybe(str),
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"ref_mask_res-2": Maybe(str),
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"T1w_template_res-2": Maybe(str),
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},
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},
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"overwrite_transform": {
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"surface_analysis": {
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"abcd_prefreesurfer_prep": {
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"run": bool1_1,
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"ref_mask_res-2": Maybe(str),
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"T1w_template_res-2": Maybe(str),
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},
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"freesurfer": {
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"run_reconall": bool1_1,

‎CPAC/resources/configs/pipeline_config_abcd-options.yml‎

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# Run freesurfer_abcd_preproc to obtain preprocessed T1w for reconall
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abcd_prefreesurfer_prep:
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run: On
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# Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
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ref_mask_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz
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# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
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T1w_template_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm.nii.gz
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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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anatomical_registration:
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run: On
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registration:
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FSL-FNIRT:
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# Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
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ref_mask_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz
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# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
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T1w_template_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm.nii.gz
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# option parameters
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ANTs:

‎CPAC/resources/configs/pipeline_config_abcd-prep.yml‎

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# Run freesurfer_abcd_preproc to obtain preprocessed T1w for reconall
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abcd_prefreesurfer_prep:
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run: On
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# Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
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ref_mask_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz
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# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
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T1w_template_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm.nii.gz
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anatomical_preproc:
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run: On
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registration_workflows:
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anatomical_registration:
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registration:
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FSL-FNIRT:
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# Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
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ref_mask_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz
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# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
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T1w_template_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm.nii.gz
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# option parameters
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ANTs:

‎CPAC/resources/configs/pipeline_config_blank.yml‎

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abcd_prefreesurfer_prep:
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run: Off
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# Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
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ref_mask_res-2: $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz
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# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
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T1w_template_res-2: $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz
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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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# It is for monkey pipeline specifically.
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FNIRT_T1w_template:
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# Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
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ref_mask_res-2: $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz
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# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
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T1w_template_res-2: $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz
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# Configuration file to be used by FSL to set FNIRT parameters.
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# It is not necessary to change this path unless you intend to use custom FNIRT parameters or a non-standard template.
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fnirt_config: T1_2_MNI152_2mm

‎CPAC/resources/cpac_templates.csv‎

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@@ -31,8 +31,8 @@ T1w-template-symmetric,"voxel_mirrored_homotopic_connectivity, symmetric_registr
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T1w-template-symmetric-deriv,"voxel_mirrored_homotopic_connectivity, symmetric_registration, T1w_template_symmetric_funcreg","Symmetric version of the T1w-based whole-head template, resampled to the desired functional derivative resolution","registration_workflows, functional_registration, func_registration_to_template, output_resolution, func_derivative_outputs"
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T1w-template-symmetric-for-resample,"voxel_mirrored_homotopic_connectivity, symmetric_registration, T1w_template_symmetric_for_resample",,
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template-ref-mask,"registration_workflows, anatomical_registration, registration, FSL-FNIRT, ref_mask",,"registration_workflows, anatomical_registration, resolution_for_anat"
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template-ref-mask-res-2,"registration_workflows, anatomical_registration, registration, FSL-FNIRT, ref_mask_res-2",,
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T1w-template-res-2,"registration_workflows, anatomical_registration, registration, FSL-FNIRT, T1w_template_res-2",,
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template-ref-mask-res-2,"surface_analysis, abcd_prefreesurfer_prep, ref_mask_res-2",,
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T1w-template-res-2,"surface_analysis, abcd_prefreesurfer_prep, T1w_template_res-2",,
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template-specification-file,"network_centrality, template_specification_file",Binary ROI mask for network centrality calculations,
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unet-model,"anatomical_preproc, brain_extraction, UNet, unet_model",,
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WM-path,"segmentation, tissue_segmentation, FSL-FAST, use_priors, WM_path",Template-space WM tissue prior,

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