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Set up the base format for the nodeblock descriptor YAML files.
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CPAC/anat_preproc/anat_preproc.yml

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# This is a C-PAC nodeblock descriptor file.
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Non-Local Means (NLM) Filtering:
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description:
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Performs non-local means filtering on structural data.
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references:
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https://en.wikipedia.org/wiki/Non-local_means
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method:
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nlm_filtering:
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description:
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Uses ANTs DenoiseImage.
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references:
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https://manpages.debian.org/experimental/ants/DenoiseImage.1.en.html
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config:
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None
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operations:
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Mermaid syntax here
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source:
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NiWrap: https://github.com/childmindresearch/cpac_blocks/blob/main/anat_preproc/nlm.py
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Nipype: https://github.com/FCP-INDI/C-PAC/blob/rc/v1.8.7/CPAC/anat_preproc/anat_preproc.py#L1528-L1537
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validation:
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s3://path/to/gold/standard
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T1w Brain Mask Generation:
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description:
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Generates a binary brain mask of a T1w structural image.
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references:
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None
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method:
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brain_mask_fsl:
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description:
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Uses FSL BET.
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references:
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- links to manuals
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- links to papers
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- etc.
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config:
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Robustfov: Off
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frac: 0.5
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mesh_boolean: Off
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outline: Off
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padding: Off
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radius: 0
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reduce_bias: Off
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remove_eyes: Off
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robust: Off
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skull: Off
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surfaces: Off
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threshold: Off
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vertical_gradient: 0.0
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operations:
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Mermaid syntax here
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source:
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validation:
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brain_mask_afni:
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description:
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Uses AFNI 3dSkullStrip.
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references:
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- links to manuals
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- links to papers
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- etc.
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config:
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shrink_factor: 0.6
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var_shrink_fac: On
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shrink_factor_bot_lim: 0.4
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avoid_vent: On
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n_iterations: 250
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pushout: On
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touchup: On
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fill_hole: 10
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NN_smooth: 72
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smooth_final: 20
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avoid_eyes: On
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use_edge: On
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exp_frac: 0.1
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push_to_edge: Off
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use_skull: Off
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perc_int: 0
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max_inter_iter: 4
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fac: 1
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blur_fwhm: 0
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monkey: Off
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operations:
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Mermaid syntax here
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source:
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validation:
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ACPC Alignment:
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description:
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ACPC alignment is meant to ... etc.
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references:
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- links to pages/tutorials generically about ACPC alignment
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method:
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acpc_alignment_head:
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description:
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More specific info (if needed)
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references:
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config:
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operations:
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source:
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validation:
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acpc_alignment_head_with_mask:
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description:
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references:
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config:
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operations:
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source:
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validation:
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