From 3f109c8da6d8e13c1a626c712efb2f971b149bec Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 8 Jul 2024 13:41:47 +0000 Subject: [PATCH 1/3] Bump version to 1.5.0-pre.46 --- hippunfold/config/snakebids.yml | 2 +- hippunfold/pipeline_description.json | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index a9fa2b3a..a75d7503 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -128,7 +128,7 @@ parse_args: --version: help: 'Print the version of HippUnfold' action: version - version: "1.4.2-pre.45" + version: "1.5.0-pre.46" --modality: diff --git a/hippunfold/pipeline_description.json b/hippunfold/pipeline_description.json index add63696..100d0daa 100644 --- a/hippunfold/pipeline_description.json +++ b/hippunfold/pipeline_description.json @@ -5,7 +5,7 @@ "GeneratedBy": [ { "Name": "hippunfold", - "Version": "1.4.2-pre.45", + "Version": "1.5.0-pre.46", "CodeURL": "https://github.com/khanlab/hippunfold", "Author": "Jordan DeKraker & Ali Khan", "AuthorEmail": "ali.khan@uwo.ca" diff --git a/pyproject.toml b/pyproject.toml index ca4a7b6d..2d42ff14 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "hippunfold" -version = "1.4.2-pre.45" +version = "1.5.0-pre.46" description = "BIDS App for Hippocampal AutoTop (automated hippocampal unfolding and subfield segmentation)" authors = ["Jordan DeKraker & Ali Khan "] From 9d4d7ada9fadbe150afaa0b35cf40d1bcae0233f Mon Sep 17 00:00:00 2001 From: Jordan DeKraker Date: Mon, 8 Jul 2024 12:06:01 -0400 Subject: [PATCH 2/3] 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 From 04e4d79926e65002dfc625ad5bd2b801fd353dc0 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 8 Jul 2024 16:06:20 +0000 Subject: [PATCH 3/3] Bump version to 1.5.0-pre.47 --- hippunfold/config/snakebids.yml | 2 +- hippunfold/pipeline_description.json | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index 360ec999..ce342260 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -128,7 +128,7 @@ parse_args: --version: help: 'Print the version of HippUnfold' action: version - version: "1.5.0-pre.46" + version: "1.5.0-pre.47" --modality: diff --git a/hippunfold/pipeline_description.json b/hippunfold/pipeline_description.json index 100d0daa..8f67d839 100644 --- a/hippunfold/pipeline_description.json +++ b/hippunfold/pipeline_description.json @@ -5,7 +5,7 @@ "GeneratedBy": [ { "Name": "hippunfold", - "Version": "1.5.0-pre.46", + "Version": "1.5.0-pre.47", "CodeURL": "https://github.com/khanlab/hippunfold", "Author": "Jordan DeKraker & Ali Khan", "AuthorEmail": "ali.khan@uwo.ca" diff --git a/pyproject.toml b/pyproject.toml index 2d42ff14..d4ec5c5a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "hippunfold" -version = "1.5.0-pre.46" +version = "1.5.0-pre.47" description = "BIDS App for Hippocampal AutoTop (automated hippocampal unfolding and subfield segmentation)" authors = ["Jordan DeKraker & Ali Khan "]