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set rat-specific defaults for FD calculations #1005

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merged 3 commits into from Aug 18, 2022
Merged

set rat-specific defaults for FD calculations #1005

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8040eae
fix: set default fd radius for rats
eilidhmacnicol Jul 18, 2022
9b516ed
sty: flake8
eilidhmacnicol Jul 21, 2022
54c6425
fix: remove call to `opts.fd_radius`
eilidhmacnicol Aug 3, 2022
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4 changes: 4 additions & 0 deletions mriqc/cli/parser.py
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Expand Up @@ -559,6 +559,10 @@ def parse_args(args=None, namespace=None):
# TODO: add other species once rats are working
if opts.species.lower() == "rat":
config.workflow.template_id = "Fischer344"
# mean distance from the lateral edge to the center of the brain is
# ~ PA:10 mm, LR:7.5 mm, and IS:5 mm (see DOI: 10.1089/089771503770802853)
# roll movement is most likely to occur, so set to 7.5 mm
config.workflow.fd_radius = 7.5
config.workflow.headmask = "NoBET"
# block uploads for the moment; can be reversed before wider release
config.execution.no_sub = True
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