diff --git a/CHANGELOG.md b/CHANGELOG.md index 85b0b6523..fa96ca94a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Moved `pygraphviz` from requirements to `graphviz` optional dependencies group. - Automatically tag untagged `subject_id` and `unique_id` as `!!str` when loading data config files. - Made orientation configurable (was hard-coded as "RPI"). +- Moved `ref_mask_res_2` and `T1w_template_res-2` fields from registration into surface under `abcd_prefreesurfer_prep`. ### Fixed diff --git a/CPAC/pipeline/schema.py b/CPAC/pipeline/schema.py index 997c6267b..cdb72747d 100644 --- a/CPAC/pipeline/schema.py +++ b/CPAC/pipeline/schema.py @@ -712,8 +712,6 @@ def sanitize(filename): "interpolation": In({"trilinear", "sinc", "spline"}), "identity_matrix": Maybe(str), "ref_mask": Maybe(str), - "ref_mask_res-2": Maybe(str), - "T1w_template_res-2": Maybe(str), }, }, "overwrite_transform": { @@ -816,6 +814,8 @@ def sanitize(filename): "surface_analysis": { "abcd_prefreesurfer_prep": { "run": bool1_1, + "ref_mask_res-2": Maybe(str), + "T1w_template_res-2": Maybe(str), }, "freesurfer": { "run_reconall": bool1_1, diff --git a/CPAC/resources/configs/pipeline_config_abcd-options.yml b/CPAC/resources/configs/pipeline_config_abcd-options.yml index 1cb360cdc..937ab7a63 100644 --- a/CPAC/resources/configs/pipeline_config_abcd-options.yml +++ b/CPAC/resources/configs/pipeline_config_abcd-options.yml @@ -32,6 +32,12 @@ surface_analysis: abcd_prefreesurfer_prep: run: On + # Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. + ref_mask_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz + + # Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. + T1w_template_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm.nii.gz + # Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives. # If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline, # select those 'Freesurfer-' labeled options further below in anatomical_preproc. @@ -102,13 +108,6 @@ registration_workflows: anatomical_registration: run: On registration: - FSL-FNIRT: - - # Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. - ref_mask_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz - - # Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. - T1w_template_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm.nii.gz # option parameters ANTs: diff --git a/CPAC/resources/configs/pipeline_config_abcd-prep.yml b/CPAC/resources/configs/pipeline_config_abcd-prep.yml index d6542ea35..32ba79bea 100644 --- a/CPAC/resources/configs/pipeline_config_abcd-prep.yml +++ b/CPAC/resources/configs/pipeline_config_abcd-prep.yml @@ -32,6 +32,12 @@ surface_analysis: abcd_prefreesurfer_prep: run: On + # Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. + ref_mask_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz + + # Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. + T1w_template_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm.nii.gz + anatomical_preproc: run: On acpc_alignment: @@ -72,13 +78,6 @@ anatomical_preproc: registration_workflows: anatomical_registration: registration: - FSL-FNIRT: - - # Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. - ref_mask_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz - - # Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. - T1w_template_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm.nii.gz # option parameters ANTs: diff --git a/CPAC/resources/configs/pipeline_config_blank.yml b/CPAC/resources/configs/pipeline_config_blank.yml index 454d8add5..5b7f3f518 100644 --- a/CPAC/resources/configs/pipeline_config_blank.yml +++ b/CPAC/resources/configs/pipeline_config_blank.yml @@ -209,6 +209,12 @@ surface_analysis: abcd_prefreesurfer_prep: run: Off + # Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. + ref_mask_res-2: $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz + + # Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. + T1w_template_res-2: $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz + # Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives. # If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline, # select those 'Freesurfer-' labeled options further below in anatomical_preproc. @@ -580,12 +586,6 @@ registration_workflows: # It is for monkey pipeline specifically. FNIRT_T1w_template: - # Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. - ref_mask_res-2: $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz - - # Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. - T1w_template_res-2: $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz - # Configuration file to be used by FSL to set FNIRT parameters. # It is not necessary to change this path unless you intend to use custom FNIRT parameters or a non-standard template. fnirt_config: T1_2_MNI152_2mm diff --git a/CPAC/resources/configs/pipeline_config_default.yml b/CPAC/resources/configs/pipeline_config_default.yml index b7aa56c13..3d067fbbc 100644 --- a/CPAC/resources/configs/pipeline_config_default.yml +++ b/CPAC/resources/configs/pipeline_config_default.yml @@ -197,6 +197,12 @@ surface_analysis: abcd_prefreesurfer_prep: run: Off + # Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. + ref_mask_res-2: $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz + + # Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. + T1w_template_res-2: $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz + # Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives. # If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline, # select those 'Freesurfer-' labeled options further below in anatomical_preproc. @@ -738,12 +744,6 @@ registration_workflows: # It is not necessary to change this path unless you intend to use a different template. identity_matrix: $FSLDIR/etc/flirtsch/ident.mat - # Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. - ref_mask_res-2: $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz - - # Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. - T1w_template_res-2: $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz - overwrite_transform: run: Off diff --git a/CPAC/resources/configs/pipeline_config_fmriprep-options.yml b/CPAC/resources/configs/pipeline_config_fmriprep-options.yml index 555b52302..f97bcf318 100644 --- a/CPAC/resources/configs/pipeline_config_fmriprep-options.yml +++ b/CPAC/resources/configs/pipeline_config_fmriprep-options.yml @@ -151,12 +151,6 @@ registration_workflows: registration: FSL-FNIRT: - # Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. - ref_mask_res-2: - - # Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline. - T1w_template_res-2: - # Reference mask for FSL registration. ref_mask: diff --git a/CPAC/resources/cpac_templates.csv b/CPAC/resources/cpac_templates.csv index 5c2abc994..cf4cad758 100644 --- a/CPAC/resources/cpac_templates.csv +++ b/CPAC/resources/cpac_templates.csv @@ -31,8 +31,8 @@ T1w-template-symmetric,"voxel_mirrored_homotopic_connectivity, symmetric_registr 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" T1w-template-symmetric-for-resample,"voxel_mirrored_homotopic_connectivity, symmetric_registration, T1w_template_symmetric_for_resample",, template-ref-mask,"registration_workflows, anatomical_registration, registration, FSL-FNIRT, ref_mask",,"registration_workflows, anatomical_registration, resolution_for_anat" -template-ref-mask-res-2,"registration_workflows, anatomical_registration, registration, FSL-FNIRT, ref_mask_res-2",, -T1w-template-res-2,"registration_workflows, anatomical_registration, registration, FSL-FNIRT, T1w_template_res-2",, +template-ref-mask-res-2,"surface_analysis, abcd_prefreesurfer_prep, ref_mask_res-2",, +T1w-template-res-2,"surface_analysis, abcd_prefreesurfer_prep, T1w_template_res-2",, template-specification-file,"network_centrality, template_specification_file",Binary ROI mask for network centrality calculations, unet-model,"anatomical_preproc, brain_extraction, UNet, unet_model",, WM-path,"segmentation, tissue_segmentation, FSL-FAST, use_priors, WM_path",Template-space WM tissue prior,