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💡 Update comments based on default preconfig
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‎CPAC/resources/configs/pipeline_config_abcd-options.yml‎

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@@ -97,13 +97,6 @@ registration_workflows:
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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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# Reference mask for FSL registration.
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ref_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask_dil.nii.gz
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# Identity matrix used during FSL-based resampling of anatomical-space data throughout the pipeline.
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# It is not necessary to change this path unless you intend to use a different template.
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identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
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# option parameters
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ANTs:
109102

@@ -183,10 +176,6 @@ registration_workflows:
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# It is not necessary to change this path unless you intend to use a non-standard template.
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T1w_brain_template: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_${resolution_for_anat}_brain.nii.gz
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# Template to be used during registration.
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# It is not necessary to change this path unless you intend to use a non-standard template.
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T1w_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
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# Template to be used during registration.
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# It is not necessary to change this path unless you intend to use a non-standard template.
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T1w_brain_template_mask: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
@@ -205,12 +194,6 @@ registration_workflows:
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# input: ['Mean_Functional', 'Selected_Functional_Volume', 'fmriprep_reference']
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input: [Selected_Functional_Volume]
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boundary_based_registration:
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# Standard FSL 5.0 Scheduler used for Boundary Based Registration.
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# It is not necessary to change this path unless you intend to use non-standard MNI registration.
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bbr_schedule: $FSLDIR/etc/flirtsch/bbr.sch
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# reference: 'brain' or 'restore-brain'
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# In ABCD-options pipeline, 'restore-brain' is used as coregistration reference
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reference: restore-brain
@@ -274,19 +257,6 @@ registration_workflows:
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# Possible values: Linear, BSpline, LanczosWindowedSinc
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interpolation: Linear
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FNIRT_pipelines:
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# Identity matrix used during FSL-based resampling of functional-space data throughout the pipeline.
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# It is not necessary to change this path unless you intend to use a different template.
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identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
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EPI_registration:
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FSL-FNIRT:
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# Identity matrix used during FSL-based resampling of BOLD-space data throughout the pipeline.
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# It is not necessary to change this path unless you intend to use a different template.
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identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
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functional_preproc:
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run: On
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motion_estimates_and_correction:
@@ -321,9 +291,6 @@ functional_preproc:
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using: [PhaseDiff, Blip-FSL-TOPUP]
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func_masking:
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FSL_AFNI:
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brain_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
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brain_probseg: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
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# Apply functional mask in native space
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apply_func_mask_in_native_space: Off

‎CPAC/resources/configs/pipeline_config_anat-only.yml‎

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@@ -77,15 +77,15 @@ registration_workflows:
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FSL-FNIRT:
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# Reference mask for FSL registration.
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ref_mask: $$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask_dil.nii.gz
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ref_mask: $$$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask_dil.nii.gz
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# Template to be used during registration.
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# It is not necessary to change this path unless you intend to use a non-standard template.
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T1w_brain_template: $$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz
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T1w_brain_template: $$$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz
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# Template to be used during registration.
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# It is not necessary to change this path unless you intend to use a non-standard template.
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T1w_template: $$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
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T1w_template: $$$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
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# Register skull-on anatomical image to a template.
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reg_with_skull: Off
@@ -112,11 +112,11 @@ registration_workflows:
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# Standard Skull Stripped Template. Used as a reference image for functional registration.
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# This can be different than the template used as the reference/fixed for T1-to-template registration.
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T1w_brain_template_funcreg: $$FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
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T1w_brain_template_funcreg: $$$FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
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# Standard Anatomical Brain Image with Skull.
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# This can be different than the template used as the reference/fixed for T1-to-template registration.
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T1w_template_funcreg: $$FSLDIR/data/standard/MNI152_T1_${func_resolution}.nii.gz
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T1w_template_funcreg: $$$FSLDIR/data/standard/MNI152_T1_${func_resolution}.nii.gz
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EPI_registration:
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ANTs:
@@ -129,7 +129,7 @@ registration_workflows:
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# Identity matrix used during FSL-based resampling of BOLD-space data throughout the pipeline.
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# It is not necessary to change this path unless you intend to use a different template.
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identity_matrix: $$FSLDIR/etc/flirtsch/ident.mat
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identity_matrix: $$$FSLDIR/etc/flirtsch/ident.mat
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functional_preproc:
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run: Off

‎CPAC/resources/configs/pipeline_config_benchmark-ANTS.yml‎

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@@ -73,9 +73,6 @@ anatomical_preproc:
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acpc_alignment:
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T1w_brain_ACPC_template: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
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# ACPC aligned template
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T1w_ACPC_template: $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz
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brain_extraction:
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run: On
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FSL-BET:
@@ -100,33 +97,6 @@ segmentation:
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registration_workflows:
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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: $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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# Reference mask for FSL registration.
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ref_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask_dil.nii.gz
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# Identity matrix used during FSL-based resampling of anatomical-space data throughout the pipeline.
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# It is not necessary to change this path unless you intend to use a different template.
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identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
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# Template to be used during registration.
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# It is not necessary to change this path unless you intend to use a non-standard template.
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T1w_brain_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz
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# Template to be used during registration.
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# It is not necessary to change this path unless you intend to use a non-standard template.
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T1w_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
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# Template to be used during registration.
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# It is not necessary to change this path unless you intend to use a non-standard template.
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T1w_brain_template_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
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# Register skull-on anatomical image to a template.
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reg_with_skull: Off
@@ -142,10 +112,6 @@ registration_workflows:
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# run: [On, Off] - this will run both and fork the pipeline
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run: [On]
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# Standard FSL 5.0 Scheduler used for Boundary Based Registration.
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# It is not necessary to change this path unless you intend to use non-standard MNI registration.
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bbr_schedule: $FSLDIR/etc/flirtsch/bbr.sch
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func_registration_to_template:
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# these options modify the application (to the functional data), not the calculation, of the
@@ -160,34 +126,6 @@ registration_workflows:
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# thus, a higher resolution may not result in a large increase in RAM needs as above
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func_derivative_outputs: 2mm
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target_template:
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T1_template:
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# Standard Skull Stripped Template. Used as a reference image for functional registration.
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# This can be different than the template used as the reference/fixed for T1-to-template registration.
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T1w_brain_template_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
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# Standard Anatomical Brain Image with Skull.
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# This can be different than the template used as the reference/fixed for T1-to-template registration.
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T1w_template_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}.nii.gz
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# Template to be used during registration.
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# It is not necessary to change this path unless you intend to use a non-standard template.
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T1w_brain_template_mask_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain_mask.nii.gz
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FNIRT_pipelines:
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# Identity matrix used during FSL-based resampling of functional-space data throughout the pipeline.
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# It is not necessary to change this path unless you intend to use a different template.
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identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
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EPI_registration:
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FSL-FNIRT:
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# Identity matrix used during FSL-based resampling of BOLD-space data throughout the pipeline.
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# It is not necessary to change this path unless you intend to use a different template.
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identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
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functional_preproc:
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run: On
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slice_timing_correction:
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# run: [On, Off] - this will run both and fork the pipeline
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run: [On]
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func_masking:
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FSL_AFNI:
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brain_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
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brain_probseg: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
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generate_func_mean:
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# Generate mean functional image

‎CPAC/resources/configs/pipeline_config_benchmark-FNIRT.yml‎

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@@ -78,9 +78,6 @@ anatomical_preproc:
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acpc_alignment:
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T1w_brain_ACPC_template: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
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# ACPC aligned template
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T1w_ACPC_template: $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz
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brain_extraction:
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run: On
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@@ -106,20 +103,6 @@ registration_workflows:
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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: $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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# Reference mask for FSL registration.
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ref_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask_dil.nii.gz
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# Identity matrix used during FSL-based resampling of anatomical-space data throughout the pipeline.
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# It is not necessary to change this path unless you intend to use a different template.
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identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
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# using: ['ANTS', 'FSL', 'FSL-linear']
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# this is a fork point
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# ANTs parameters for T1-template-based registration
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T1_registration:
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# Template to be used during registration.
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# It is not necessary to change this path unless you intend to use a non-standard template.
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T1w_brain_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz
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# Template to be used during registration.
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# It is not necessary to change this path unless you intend to use a non-standard template.
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T1w_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
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# Template to be used during registration.
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# It is not necessary to change this path unless you intend to use a non-standard template.
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T1w_brain_template_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
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# Register skull-on anatomical image to a template.
148119
reg_with_skull: Off
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# run: [On, Off] - this will run both and fork the pipeline
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run: [On]
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# Standard FSL 5.0 Scheduler used for Boundary Based Registration.
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# It is not necessary to change this path unless you intend to use non-standard MNI registration.
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bbr_schedule: $FSLDIR/etc/flirtsch/bbr.sch
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func_registration_to_template:
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# these options modify the application (to the functional data), not the calculation, of the
@@ -176,40 +143,13 @@ registration_workflows:
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# thus, a higher resolution may not result in a large increase in RAM needs as above
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func_derivative_outputs: 2mm
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179-
target_template:
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T1_template:
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# Standard Skull Stripped Template. Used as a reference image for functional registration.
183-
# This can be different than the template used as the reference/fixed for T1-to-template registration.
184-
T1w_brain_template_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
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# Standard Anatomical Brain Image with Skull.
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# This can be different than the template used as the reference/fixed for T1-to-template registration.
188-
T1w_template_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}.nii.gz
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# Template to be used during registration.
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# It is not necessary to change this path unless you intend to use a non-standard template.
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T1w_brain_template_mask_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain_mask.nii.gz
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FNIRT_pipelines:
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# Identity matrix used during FSL-based resampling of functional-space data throughout the pipeline.
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# It is not necessary to change this path unless you intend to use a different template.
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identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
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200146
EPI_registration:
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ANTs:
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203149
# EPI registration configuration - synonymous with T1_registration
204150
# parameters under anatomical registration above
205151
parameters:
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FSL-FNIRT:
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# Identity matrix used during FSL-based resampling of BOLD-space data throughout the pipeline.
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# It is not necessary to change this path unless you intend to use a different template.
211-
identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
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functional_preproc:
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run: On
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slice_timing_correction:
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# run: [On, Off] - this will run both and fork the pipeline
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run: [On]
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func_masking:
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FSL_AFNI:
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brain_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
234-
brain_probseg: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
235-
236171
generate_func_mean:
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238173
# Generate mean functional image

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