[论文精读]The minimal preprocessing pipelines for the Human Connectome Project

论文原文：The minimal preprocessing pipelines for the Human Connectome Project - ScienceDirect

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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

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

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