diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index af648e51..be0487ec 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -418,12 +418,12 @@ template_files: dseg: tpl-ABAv3_hemi-{hemi}_space-corobl_desc-tissuemanual_dseg.nii.gz coords: tpl-ABAv3_dir-{dir}_hemi-{hemi}_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz bigbrain: - T1w: tpl-bbhist_100um_T1w.nii.gz - xfm_corobl: tpl-bbhist_from-native_to-corobl_type-itk_affine.txt - crop_ref: tpl-bbhist_hemi-{hemi}_space-corobl_desc-tissuemanual_40um_dseg.nii.gz - Mask_crop: tpl-bbhist_hemi-{hemi}_space-corobl_desc-tissuemanual_40um_dseg.nii.gz - dseg: tpl-bbhist_hemi-{hemi}_space-corobl_desc-tissuemanual_40um_dseg.nii.gz - coords: tpl-bbhist_dir-{dir}_hemi-{hemi}_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz + T1w: tpl-bigbrain_100um_T1w.nii.gz + xfm_corobl: tpl-bigbrain_from-native_to-corobl_type-itk_affine.txt + crop_ref: tpl-bigbrain_hemi-{hemi}_space-corobl_desc-tissuemanual_40um_dseg.nii.gz + Mask_crop: tpl-bigbrain_hemi-{hemi}_space-corobl_desc-tissuemanual_40um_dseg.nii.gz + dseg: tpl-bigbrain_hemi-{hemi}_space-corobl_desc-tissuemanual_40um_dseg.nii.gz + coords: tpl-bigbrain_dir-{dir}_hemi-{hemi}_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz atlas_files: multihist7: diff --git a/hippunfold/workflow/rules/preproc_manualseg.smk b/hippunfold/workflow/rules/preproc_manualseg.smk index 7467c48c..94b60a4f 100644 --- a/hippunfold/workflow/rules/preproc_manualseg.smk +++ b/hippunfold/workflow/rules/preproc_manualseg.smk @@ -4,9 +4,10 @@ rule import_manualseg_to_corobl: in_img=partial(get_single_bids_input, component="manualseg"), template_dir=Path(download_dir) / "template" / config["template"], params: - std_to_cor=lambda wildcards: config["template_files"][config["template"]][ - "xfm_corobl" - ].format(**wildcards), + std_to_cor=lambda wildcards, input: Path(input.template_dir) + / config["template_files"][config["template"]]["xfm_corobl"].format( + **wildcards + ), ref=lambda wildcards, input: Path(input.template_dir) / config["template_files"][config["template"]]["crop_ref"].format(**wildcards), output: