diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index a9286f86..29c12c79 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -190,9 +190,15 @@ parse_args: default: false action: store_true + --crop_native_res: + help: 'Sets the bounding box resolution for the crop native (e.g. cropT1w space). Under the hood, hippUnfold operates at higher resolution than the native image, so this tries to preserve some of that detail. (default: %(default)s)' + default: '0.2x0.2x0.2mm' + --crop_native_box: - help: 'Sets the bounding box size for the crop native (e.g. cropT1w) space). Make this larger if your hippocampi in crop{T1w,T2w} space are getting cut-off (default: %(default)s)' - default: '256x256x256vox' + help: 'Sets the bounding box size for the crop native (e.g. cropT1w space). Make this larger if your hippocampi in crop{T1w,T2w} space are getting cut-off (default: %(default)s)' + default: '52x52x52mm' + + --atlas: choices: @@ -386,7 +392,8 @@ nnunet_model: hippb500: trained_model.3d_fullres.Task110_hcp1200_b1000crop.nnUNetTrainerV2.model_best.tar neonateT1w: trained_model.3d_fullres.Task205_hcp1200_b1000_finetuneround2_dhcp_T1w.nnUNetTrainerV2.model_best.tar -crop_native_box: '256x256x256vox' +crop_native_box: '52x52x52mm' +crop_native_res: '0.2x0.2x0.2mm' hippdwi_opts: resample_dim: '734x720x67' # from 220x216x20 @ 1x1x1mm -> 0.3mm diff --git a/hippunfold/workflow/rules/resample_final_to_crop_native.smk b/hippunfold/workflow/rules/resample_final_to_crop_native.smk index b8c9fbb6..e583be93 100644 --- a/hippunfold/workflow/rules/resample_final_to_crop_native.smk +++ b/hippunfold/workflow/rules/resample_final_to_crop_native.smk @@ -17,7 +17,7 @@ rule create_native_crop_ref: allow_missing=True, ), params: - resample="400%", + resample=config["crop_native_res"], pad_to=config["crop_native_box"], output: ref=bids(