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bigbrain template laplace coords added #309

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Jul 8, 2024
Merged

bigbrain template laplace coords added #309

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15 changes: 14 additions & 1 deletion hippunfold/config/snakebids.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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)'

Expand All @@ -164,6 +165,7 @@ parse_args:
- 'MBMv3'
- 'CIVM'
- 'ABAv3'
- 'bigbrain'
default: 'upenn'
help: 'Set the template to use for shape injection. (default: %(default)s)'

Expand Down Expand Up @@ -400,7 +402,10 @@ template_based_segmentation:
hemi:
- R
- L

bigbrain:
hemi:
- R
- L

template_files:
CITI168:
Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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


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