From 9d4d7ada9fadbe150afaa0b35cf40d1bcae0233f Mon Sep 17 00:00:00 2001 From: Jordan DeKraker Date: Mon, 8 Jul 2024 12:06:01 -0400 Subject: [PATCH] bigbrain template laplace coords added (#309) Co-authored-by: Jordan DeKraker --- hippunfold/config/snakebids.yml | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index a75d7503..360ec999 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -151,6 +151,7 @@ parse_args: - 'MBMv3' - 'CIVM' - 'ABAv3' + - 'bigbrain' 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. When using a non-human template, consider using a corresponding atlas. (default: %(default)s)' @@ -164,6 +165,7 @@ parse_args: - 'MBMv3' - 'CIVM' - 'ABAv3' + - 'bigbrain' default: 'upenn' help: 'Set the template to use for shape injection. (default: %(default)s)' @@ -400,7 +402,10 @@ template_based_segmentation: hemi: - R - L - + bigbrain: + hemi: + - R + - L template_files: CITI168: @@ -455,6 +460,13 @@ template_files: Mask_crop: tpl-ABAv3_hemi-{hemi}_space-corobl_desc-tissuemanual_dseg.nii.gz 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 atlas_files: multihist7: @@ -558,6 +570,7 @@ resource_urls: upenn: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c1613d27b122a94ca09/?zip=' CIVM: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395bf62827451220b86e24/?zip=' ABAv3: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/6668855b6b6c8e2cc704ca97/?zip=' + bigbrain: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/666b1bc765e1de5972893e59/?zip=' #to get hash, see https://github.com/CenterForOpenScience/osf.io/issues/8256#issuecomment-379833911