From 809e027d5fe06862d6c8297ba2972fa490bb37cd Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Fri, 23 Feb 2024 14:17:12 -0500 Subject: [PATCH] update template-seg CLI message, and fix config - ensures entries in template_based_segmentation are correct (ie only include templates that have coords/dseg, and whatever hemis are available --- hippunfold/config/snakebids.yml | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index 57c7579c..4c9033c2 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -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' @@ -367,15 +367,12 @@ 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 @@ -383,7 +380,6 @@ template_based_segmentation: MBMv2: hemi: - R - - L MBMv3: hemi: - R