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example_config.yaml
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example_config.yaml
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# NOTE: see `bifrost --help` for parameter reference
parameters:
build_template:
# NOTE: parameters with null values are ignored, set to non-null value to override defaults
reference_image: null
affine_steps: null
syn_steps: null
gradient_step: null
preprocessing: 'CLAHE'
# mirror is a boolean ("store_true" action) parameter, any non-null non-boolean values will be parsed as true
mirror: true
# NOTE: the --downsample_to parameter is ommitted from all registration steps
# due to potential interaction with other steps. You are advised to downsample
# images as necessary prior to execution of the pipeline
register_template_to_fda:
clahe_kernel_size: null
moving_clip_limit: -1
fixed_clip_limit: -1
# mirror_warp is a boolean parameter, any non-null non-boolean values will be parsed as true
mirror_warp: true
register_structural_images_to_template:
clahe_kernel_size: null
moving_clip_limit: -1
fixed_clip_limit: -1
# mirror_warp is a boolean ("store_true" action) parameter, any non-null non-boolean values will be parsed as true
mirror_warp: false
# skip_synthmorph is a boolean ("store_true" action) parameter, any non-null non-boolean values will be parsed as true
# for this step you probably want to leave set to True
skip_synthmorph: true
transform_dependent_images_to_template:
apply_preprocessing: false
transform_dependent_images_to_fda:
apply_preprocessing: false
# NOTE: all other resource declarations are to be made in the cluster profile
# threads are declared separately to allow requested threads to be turned down
# for less computationally-intensive rules
resources:
# max threads available to bifrost, you should set this value to the number of
# cores available in the nodes on your cluster
max_threads: 16