论文原文：The minimal preprocessing pipelines for the Human Connectome Project - ScienceDirect
未完待续
1. 论文逐段精读
1.1. Abstract
①The Human Connectome Project (HCP) includes multiple magnetic resonance imaging (MRI) data
②HCP needs more preprocessing pipelines such as spatial artifact/distortion removal, surface generation, cross-modal registration and alignment to standard space
③CIFTI file format and the associated grayordinate spatial coordinate system is their final output
1.2. Introduction and rationale
①Imaging modalities contain:
| a) T1-weighted (T1w) and T2-weighted (T2w) structural scans |
| b) resting-state and task-based functional MRI scans |
| c) diffusion-weighted MRI scans |
②Even though unprocessed data can be directdly used in analysis, processed might bring better results and reduce error
③It is necessary for HCP in different stages to use different processing approaches
④The authors propose 6 minimal (i.e. minimize the amount of deleted information) pre-processing pipelines for
| a) removing spatial artifacts and distortions |
| b) generating cortical surfaces, segmentations, and myelin maps |
| c) making the data easily viewable in the Connectome Workbench visualization software |
| d) generating precise within-subject cross-modal registrations |
| e) handling surface and volume cross-subject registrations to standard volume and surface spaces |
| f) making the data available in the CIFTI format in a standard “grayordinate” space |
consortium n.(合作进行某项工程的)财团，银团，联营企业；联盟 (复数：consortia)
esoteric adj.秘传的；机密的, 隐秘的；只有内行才懂的；具神秘教义的
oblique adj.斜的；间接的，拐弯抹角的 n.倾斜物；斜线符 vi.倾斜 adv.成45度角地
1.3. The CIFTI file format and grayordinates, a combined cortical surface and subcortical volume coordinate system
①They think 2D geodesic distances are better than 3D Euclidean distances in that brains are always full of sulcus
②The 3D subcortical structure is best analyzed in 3D volume space
③The Connectivity Informatics Technology Initiative (CIFTI) file format stores gray matter data
④Standard grayordinate space is the combination of a set of standard subcortical volume parcels and the right and left standard cortical surface meshes. The picture below is CIFTI:
⑤Most CIFTI file includes 2D matrix, the one dimension is spatial domain (often the standard set of grayordinates). For instance, row represents spatial dimensionality and column represents time potint in dense timeseries file. However, in dense Connectome file, the two dimensionalities are spatial domain.
⑥Dense timeseries file:
⑦Dense Connectome file:
⑧If only need to perform independent analysis of each grayscale without referring to the spatial relationship between grayscales, CIFTI file can be converted to NIFTI-1 file
⑨NIFTI can be split into GIFTI surface data and NIFTI volume data
geodesic adj.测地线的，大地线的(曲面上两点间距离最短的线) n.【数】同“geodesic line”
cerebral adj.脑的;大脑的;智力的;理智的 sulcal adj.沟的
thalamus n.丘脑;视丘;背侧丘脑
1.4. HCP structural acquisitions
1.5. HCP functional and diffusion acquisitions
1.6. HCP pipelines: minimum acquisition requirements
1.7. HCP pipelines
1.8. HCP pipelines: overview
1.9. HCP pipelines: PreFreeSurfer
1.10. HCP pipelines: FreeSurfer
1.11. HCP pipelines: PostFreeSurfer
1.12. HCP pipelines: fMRIVolume
1.13. HCP pipelines: fMRISurface
1.14. HCP pipelines: Diffusion Preprocessing
1.15. Future directions for the HCP minimal preprocessing pipelines
2. 知识补充
3. Reference List
Glasser, M. F. et al. (2013) 'The minimal preprocessing pipelines for the Human Connectome Project', NeuroImage, vol. 80, pp. 105-124. doi: Redirecting
