From a066e7561f8066d7d964efcbf543eeed5154c1f3 Mon Sep 17 00:00:00 2001 From: Jordan DeKraker Date: Wed, 12 Jun 2024 11:43:17 -0400 Subject: [PATCH] added marmoset template (#297) Co-authored-by: Jordan DeKraker --- hippunfold/config/snakebids.yml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index 7ceffb98..0a2a97f6 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -152,8 +152,7 @@ parse_args: - 'CIVM' - 'ABAv3' default: 'CITI168' - help: 'Set the template to use for registration to coronal oblique (and optionally for template-based segmentation if --use-template-seg is enabled). CITI168 is for adult human data, dHCP is for neonatal human data, MBMv2 is for ex vivo marmoset data, MBMv3 is for in vivo marmoset data, CIVM is for in vivo macaque data, and ABAv3 is for mouse data. (default: %(default)s)' - + help: 'Set the template to use for registration to coronal oblique (and optionally for template-based segmentation if --use-template-seg is enabled). CITI168 is for adult human data, dHCP is for neonatal human data, MBMv2 is for ex vivo marmoset data, MBMv3 is for in vivo marmoset data, CIVM is for in vivo macaque data, and ABAv3 is for mouse data. When using a non-human template, consider using a corresponding atlas. (default: %(default)s)' @@ -233,6 +232,7 @@ parse_args: - 'magdeburg' - 'freesurfer' - 'multihist7' + - 'macaque' - 'mouse' default: - 'multihist7' @@ -465,6 +465,10 @@ atlas_files: label_nii: sub-all_hemi-{hemi}_space-unfold_label-hipp_desc-freesurfersubfields_dseg.nii.gz lut: desc-subfields_atlas-mfreesurfer_dseg.tsv label_list: freesurfer_labellist.txt + macaque: + label_nii: sub-bigmac_hemi-{hemi}_space-unfold_label-hipp_desc-macaquesubfields_dseg.nii.gz + lut: desc-subfields_atlas-macaque_dseg.tsv + label_list: macaque_labellist.txt mouse: label_nii: sub-ABAv3_space-unfold_label-hipp_desc-mousesubfields_dseg.nii.gz lut: desc-subfields_atlas-mouse_dseg.tsv @@ -530,6 +534,7 @@ resource_urls: bigbrain: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8b13d27b123094c96f/?zip=' magdeburg: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8013d27b122f94c938/?zip=' freesurfer: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8513d27b123094c96a/?zip=' + macaque: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/6661f504d835c42bcb4cddab/?zip=' mouse: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/666884380f8c80103a3c9569/?zip=' template: CITI168: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395bf0282745121fb86a93/?zip='