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update template-seg CLI message, and fix config
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- ensures entries in template_based_segmentation are correct (ie only
include templates that have coords/dseg, and whatever hemis are
available
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akhanf committed Feb 23, 2024
1 parent 365918d commit 809e027
Showing 1 changed file with 2 additions and 6 deletions.
8 changes: 2 additions & 6 deletions hippunfold/config/snakebids.yml
Original file line number Diff line number Diff line change
Expand Up @@ -166,7 +166,7 @@ parse_args:
help: 'Set the template to use for shape injection. (default: %(default)s)'

--use_template_seg:
help: 'Use template-based segmentation for hippocampal tissue *instead of* nnUnet and shape injection. This is only to be used if nnUnet models are not trained for the data you are using, e.g. for non-human primate data with the MBMv2 (ex vivo marmoset), MBMv3 (in vivomarmoset), or CIVM (in vivo macaque) template. (default: %(default)s)'
help: 'Use template-based segmentation for hippocampal tissue *instead of* nnUnet and shape injection. This is only to be used if nnUnet models are not trained for the data you are using, e.g. for non-human primate data with the MBMv2 (ex vivo marmoset), MBMv3 (in vivo marmoset), or CIVM (ex vivo macaque) template. (default: %(default)s)'
default: False
action: 'store_true'

Expand Down Expand Up @@ -367,23 +367,19 @@ singularity:
xfm_identity: resources/etc/identity_xfm.txt

#templates enabled for template-based segmentation are here
# TODO: should also perhaps include modalities avaialble, and any custom crop_native_res settings
template_based_segmentation:
CITI168:
hemi:
- R
- L
dHCP:
hemi:
- R
- L
CIVM:
hemi:
- R
- L
MBMv2:
hemi:
- R
- L
MBMv3:
hemi:
- R
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