Ginkgo Herlin's Deep White Matter Atlas of the Human Brain

The Deep White Matter Atlas of the Human Brain was built on the entire HCP-YA cohort, made of 1065 young healthy subjects. The construction of this atlas is based on the analysis of the anatomical and diffusion MRI acquisitions of each subject, using the tractography and fiber clustering tools available in the Ginkgo toolbox (CEA, NeuroSpin, BAOBAB, GAIA, Ginkgo Team, https://framagit.org/cpoupon/gkg). Detailed information on the construction of the atlas can be found in the related article. The atlas can be visualized with the BrainVISA/Anatomist viewer available at https://brainvisa.info/web/download.html. The atlas is registered in the MNI space.

This atlas is composed of 77 white matter tracts, including:

- 30 association tracts (15 per hemisphere): arcuate fasciculus, corticospinal tract, dorsal cingulum, ventral cingulum, long dorsoventral cingulum, external capsule, extreme capsule, frontal aslant, inferior fronto-occipital fasciculus, inferior longitudinal fasciculus, middle longitudinal fasciculus, superior longitudinal fasciculus 1, superior longitudinal fasciculus 2, superior longitudinal fasciculus 3, and uncinate fasciculus.

- 38 projection tracts (19 per hemisphere): fornix, centro-caudate tract, cingulo-caudate tract, fronto-caudate tract, parieto-caudate tract, centro-lenticular tract, fronto-lenticular tract, occipito-lenticular tract, parieto-lenticular tract, temporo-lenticular tract, spino-cerebellar tract, middle cortico-cerebellar tract, superior cortico-cerebellar tract, optic radiation, thalamo-central tract, thalamo-frontal tract, thalamo-occipital tract, thalamo-parietal tract, and thalamo-temporal tract.

- 8 inter-hemispheric tracts : anterior comissure, and 7 subdivisions of the corpus callosum according to Wittelsion segmentation (rostrum, genu, rostral body, anterior midbody, posterior midbody, isthmus, splenium)

- 1 intra-cerebellar tract : the parallel fibers.

The atlas is provided in the Anatomist *.bundles/*.bundlesdata format, for which the *.bundles file contains meta information, including:

- The labels of the different white matter bundles ('labels' entry),

- The number of streamlines populating each white matter bundle ('curve3d_counts' entry), in the same order as the 'labels' key,

- The total number of white matter bundles ('item_count' entry),

- The total number of streamlines ('curves_count' entry).

Two different versions of the atlas are provided :

- A non-symmetrized version of the atlas in which the left and right tracts retain the anatomical differences found within the HCP-YA cohort. This version is better suited for visual representation of deep white matter tracts. This atlas is referenced as "Ginkgo_Herlin_HumanDeepWhiteMatterAtlas_Unsymmetrized".

- A symmetrized version of the atlas in which the left and right tracts have been symmetrized, i.e. the left and right tracts are exactly the same with respect to an axis of symmetry along the sagital plane, and the interhemispheric tracts have been fused with their symmetric versions. This version is more suitable for tractography analysis: the atlas can be applied to a whole-brain tractogram of any subject (registered in MNI space) to automatically label the deep white matter tracts, for example using a minimum distance threshold algorithm (with the optimized distance threshold for each tract specified in the maximum-distance-to-bundle-map.py file). The symmetric version of the atlas ensures that any left-right difference found after labeling is due to a difference within the subject's tractogram and not to a difference in the atlas itself. This atlas is referenced as "Ginkgo_Herlin_HumanDeepWhiteMatterAtlas_Symmetrized".

Each atlas is provided in a high-resolution version with a fiber resampling step of 1mm, and a low-resolution version with a fiber resampling step of 3mm. This resampling step is specified at the end of the atlas filename as "_1mm" and "_3mm" respectively.

人类大脑深部白质图谱（Deep White Matter Atlas of the Human Brain）构建于完整的HCP-YA队列之上，该队列包含1065名年轻健康受试者。本图谱的构建基于对每位受试者的解剖MRI与弥散MRI采集数据的分析，使用了Ginkgo工具箱（Ginkgo toolbox，CEA、NeuroSpin、BAOBAB、GAIA及Ginkgo团队开发，https://framagit.org/cpoupon/gkg）中内置的纤维束追踪与纤维聚类工具。有关本图谱构建的详细方法，请参见配套研究论文。该图谱可通过BrainVISA/Anatomist可视化查看器进行展示，工具下载地址为https://brainvisa.info/web/download.html。本图谱已配准至MNI空间。

本图谱共包含77条白质纤维束，具体如下：
- 30条联络纤维（每侧半球15条）：弓状束、皮质脊髓束、背侧扣带、腹侧扣带、长背腹侧扣带、外囊、最外囊、额斜束、额下枕束、下纵束、中纵束、上纵束1、上纵束2、上纵束3以及钩束。
- 38条投射纤维（每侧半球19条）：穹窿、中央尾状束、扣带尾状束、额尾状束、顶尾状束、中央豆状束、额豆状束、枕豆状束、顶豆状束、颞豆状束、脊髓小脑束、中脑皮质小脑束、上脑皮质小脑束、视辐射、丘脑中央束、丘脑额叶束、丘脑枕叶束、丘脑顶叶束以及丘脑颞叶束。
- 8条半球间纤维：前联合，以及依据Wittelsion分割法划分的胼胝体7个亚区（嘴部、膝部、嘴侧体部、前中体部、后中体部、峡部、压部）。
- 1条小脑内纤维：平行纤维。

本图谱以Anatomist支持的*.bundles/*.bundlesdata格式提供，其中*.bundles文件包含元信息，具体包括：
- 不同白质纤维束的标签（对应'labels'字段），
- 每条白质纤维束所包含的纤维束流线数量（对应'curve3d_counts'字段），排序与'labels'键一致，
- 白质纤维束的总数量（对应'item_count'字段），
- 纤维束流线的总数量（对应'curves_count'字段）。

本图谱提供两种不同版本：
- 非对称版本：保留了HCP-YA队列中左右侧纤维束的解剖学差异，该版本更适合深部白质纤维束的可视化展示。该图谱命名为"Ginkgo_Herlin_HumanDeepWhiteMatterAtlas_Unsymmetrized"。
- 对称版本：将左右侧纤维束进行对称化处理，即沿矢状面的对称轴，左右侧纤维束完全一致，并将半球间纤维束与其对称版本融合。该版本更适用于纤维束追踪分析：可将本图谱应用于任何已配准至MNI空间的受试者全脑纤维束追踪结果，以自动标注深部白质纤维束，例如可通过最小距离阈值算法实现（各纤维束的优化距离阈值可在maximum-distance-to-bundle-map.py文件中获取）。该对称版本可确保标注后发现的任何左右侧差异均来自受试者自身的纤维束追踪结果，而非图谱本身的差异。该图谱命名为"Ginkgo_Herlin_HumanDeepWhiteMatterAtlas_Symmetrized"。

每种版本的图谱均提供高分辨率与低分辨率两个子版本：高分辨率版本的纤维重采样步长为1mm，低分辨率版本的纤维重采样步长为3mm。重采样步长信息会以"_1mm"和"_3mm"的形式分别附加在图谱文件名末尾。