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🎨 Use Sphinx start-at/-after and end-at/-before (#258)
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‎docs/_sources/user/after_warp.rst‎

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.. literalinclude:: /references/default_pipeline.yml
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:language: YAML
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:start-at: # OUTPUTS AND DERIVATIVES
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:end-at: output: ['z-scored']
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External Resources
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^^^^^^^^^^^^^^^^^^

‎docs/_sources/user/alff.rst‎

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.. literalinclude:: /references/default_pipeline.yml
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:language: YAML
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:start-at: amplitude_low_frequency_fluctuation:
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:end-before: regional_homogeneity:
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References
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^^^^^^^^^^

‎docs/_sources/user/anat.rst‎

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.. literalinclude:: /references/default_pipeline.yml
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:language: YAML
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:start-at: surface_analysis:
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:end-before: longitudinal_template_generation:
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Initial Preprocessing
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^^^^^^^^^^^^^^^^^^^^^
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.. literalinclude:: /references/default_pipeline.yml
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:language: YAML
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:start-at: anatomical_preproc:
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:end-before: Run ACPC alignment before non-local means filtering or N4 bias
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Configuring ACPC Alignment options:
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""""""""""""""""""""""""""""""""""""""
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.. literalinclude:: /references/default_pipeline.yml
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:start-at: anatomical_preproc:
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.. literalinclude:: /references/default_pipeline.yml
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:start-at: acpc_alignment:
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:end-before: brain_extraction:
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Skull-Stripping
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^^^^^^^^^^^^^^^
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:language: YAML
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:start-at: anatomical_preproc:
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.. literalinclude:: /references/default_pipeline.yml
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:start-at: brain_extraction:
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:end-at: using: ['3dSkullStrip']
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Configuring AFNI 3dSkullStrip options:
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""""""""""""""""""""""""""""""""""""""
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:language: YAML
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:start-at: anatomical_preproc:
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:start-at: brain_extraction:
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:lines: 1
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.. literalinclude:: /references/default_pipeline.yml
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:start-at: AFNI-3dSkullStrip:
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:end-before: FSL-BET:
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Configuring FSL BET options:
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""""""""""""""""""""""""""""
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:start-at: anatomical_preproc:
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:start-at: brain_extraction:
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:lines: 1
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.. literalinclude:: /references/default_pipeline.yml
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:start-at: FSL-BET:
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:end-before: UNet:
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Configuring niworkflows-ants options:
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"""""""""""""""""""""""""""""""""""""
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:start-at: anatomical_preproc:
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:start-at: brain_extraction:
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.. literalinclude:: /references/default_pipeline.yml
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:start-at: niworkflows-ants:
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:end-before: FreeSurfer-BET:
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Anatomical Registration
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^^^^^^^^^^^^^^^^^^^^^^^
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:language: YAML
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:start-at: registration_workflows:
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:end-before: functional_registration:
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Anatomical Tissue Segmentation
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.. literalinclude:: /references/default_pipeline.yml
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:language: YAML
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:start-at: segmentation:
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:end-before: registration_workflows:
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References
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^^^^^^^^^^

‎docs/_sources/user/aroma_ica.rst‎

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:start-at: nuisance_corrections:
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:end-before: 2-nuisance_regression:
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EXTERNAL RESOURCES:
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^^^^^^^^^^^^^^^^^^^

‎docs/_sources/user/centrality.rst‎

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:start-at: network_centrality:
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:end-before: # PACKAGE INTEGRATIONS
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References
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^^^^^^^^^^

‎docs/_sources/user/compute_config.rst‎

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:start-at: pipeline_setup:
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.. literalinclude:: /references/default_pipeline.yml
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:language: YAML
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:start-at: system_config:
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:end-before: Amazon-AWS:
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Setting up SGE
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"""""""""""""""

‎docs/_sources/user/func.rst‎

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:start-at: registration_workflows:
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:language: YAML
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:start-at: functional_registration:
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:end-before: boundary_based_registration:
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.. literalinclude:: /references/default_pipeline.yml
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:language: YAML
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:start-at: functional_preproc:
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:end-before: slice_timing_correction:
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.. literalinclude:: /references/default_pipeline.yml
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:language: YAML
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:start-at: motion_estimates_and_correction:
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:end-before: distortion_correction:
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.. _motion_estimate_filter_valid_options:
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:start-at: functional_preproc:
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:language: YAML
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:start-at: slice_timing_correction:
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:end-before: motion_estimates_and_correction:
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Through the Data Configuration
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:start-at: functional_preproc:
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:language: YAML
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:start-at: distortion_correction:
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:end-before: func_masking:
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Functional to Anatomical Registration
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:start-at: registration_workflows:
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:lines: 1
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.. literalinclude:: /references/default_pipeline.yml
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:language: YAML
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:start-at: functional_registration:
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:end-before: reference:
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.. literalinclude:: /references/default_pipeline.yml
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:language: YAML
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:start-at: func_input_prep:
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:end-before: EPI_registration:
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:language: YAML
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:start-at: functional_preproc:
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.. literalinclude:: /references/default_pipeline.yml
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:language: YAML
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:start-at: func_masking:
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:end-before: FSL-BET:
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Configuring FSL BET options:
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:language: YAML
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:start-at: functional_preproc:
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.. literalinclude:: /references/default_pipeline.yml
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:language: YAML
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:start-at: FSL-BET:
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:end-before: FSL_AFNI:
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Functional to Template Registration
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:lines: 482-483,602-603,636-812
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:start-at: registration_workflows:
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.. literalinclude:: /references/default_pipeline.yml
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:language: YAML
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:start-at: functional_registration:
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:language: YAML
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:start-at: EPI_registration:
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:end-before: ANTs_pipelines:

‎docs/_sources/user/futuredocs/epi_distcorr.rst‎

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:start-at: distortion_correction:
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:end-before: func_masking:

‎docs/_sources/user/longitudinal.rst‎

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:start-at: longitudinal_template_generation:
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:end-before: anatomical_preproc:
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References
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‎docs/_sources/user/nuisance.rst‎

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:language: YAML
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:start-at: nuisance_corrections:
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:language: YAML
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:start-at: 2-nuisance_regression:
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:end-before: # OUTPUTS AND DERIVATIVES
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An example of nuisance regressors
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