unzip解压压缩包中指定的文件

近年来,开放科学Open Science在学术圈得到越来越多的关注。在开放数据方面,研究者开始接受将采集的数据在线共享,同时越来越多的研究者开始基于在线共享的数据开展研究。

研究者通常以压缩包的形式将数据上传到网络。而在其他研究使用公开共享的数据开展研究时,由于通常情况下,该数据并非为其设计和采集,数据使用者需要将所有数据下载,并解压所有数据文件。有些时候(比如,用个人的笔记本下10几G的HCP数据),下载的压缩包本身就很大,如果全部解压,将会占用更多硬盘空间(然而,我硬盘空间不够解压所有数据了。。)。碰到这个问题,解决方案可以是将数据copy到另一台电脑或服务器,全部解压后,挑选需要的数据;另一个方案可以考虑选择性的解压一些需要的文件。本文就是笔者在使用HCP数据时,由于碰到Mac空间有限的问题,找到的解决方案。

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脑科学相关SCI Top期刊_2017

在学术成果评价中,经常会提及SCI Top期刊。SCI Top是中国科学院文献情报中心发布的中科院期刊分区中的一些排名靠前的期刊,紧随其后的期刊一般标签为SCI2,SCI3和SCI4区期刊。所谓SCI Top实际上是包括了SCI1区的期刊和部分SCI2区的期刊,其中SCI1区大致定义为领域排名前5%的期刊。由于一些领域期刊数量有限,导致SCI1区期刊屈指可数,导致SCI1区在实际的学术成果评价中可用性不大;可能是出于这一原因,中科院期刊分区单独定义了SCI Top期刊,以涵盖更多领域认可的期刊。

SCI Top 期刊

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Look Back:颞平面不对称性 Planum Temporale Asymmetry

颞平面(planum temporale)是位于颞上回(superior temporal gyrus)后部背侧皮层的一个三角形区域,其左侧脑区与经典的语言功能区Wernicke’s area存在一定的重合。一直以来,颞平面被认为是人脑皮层中结构偏侧化最明显的脑区。同时,由于广泛存在的言语和语言网络的左偏侧化,颞平面的偏侧化更被研究者与人类独特的语言能力相关联。

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p值:这个锅,我不背!

在关于重新定义显著性阈值的文章(Benjamin_2017_Redefine statistical significance)在线发表后,关于p值争论就没有停息,其中有支持,有反对,更有人提出了包括舍弃显著性阈值,甚至p值的新方案。这些争论很多来自方法学领域的领军人物,各方言辞凿凿,其中的争议可见一斑,短期内也不可能有个定论。下面是一些笔者自己关于p值与可重复性问题的random想法。

显著性

笔者认为,将显著性阈值本身是否合理,与研究结果的可重复性问题联系起来,本身就值得思考。这一联系,本身反映了一些研究者自身对p值的误解,以及这种误解的根深蒂固。

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Redefine significance? Remove it?

Benjamin等(2017)提出重新定义显著性阈值的文章发表后,在网上引起了激烈的讨论。其中,Amrhein和Greenlan在同一期刊Nature Human Behavior上对Benjamin的文章做了回应,表示我们要抛弃显著性阈值。

p<0.05 versus p<0.005

回应首先用三分法(Trichotomy)总结了Benjamin等人的建议,即p<0.005为显著(significant),p<0.05为提示性(suggestive)证据,p>0.05为不显著(nonsignificant)。这里”三分法”的提法似乎在暗讽其与传统的二分法(Dichotomy)没有多大区别。

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Redefine statistical significance? Let's just do science in a scientific way.

Lack of reproducibility of scientific studies has caused growing concern among researchers. Causes of this issue may include multiple testing, p-hacking, publication bias and under-powered studies. Another potential cause has been raised recently. That is, “statistical standards of evidence for claiming new discoveries in many fields of science are simply too low” (Benjamin et al., 2017). The paper on redefining statistical significance has been published in Nature Human Behaviour. The authors included leaders in the push for greater reproducibility. They claimed that the traditional significance (i.e., 0.05) threshold resulted in unexpected high ‘false positive’, and that reducing the p value threshold would “immediately improve reproducibility”.

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我的第一篇NeuroImage“大事记”

先晒文章信息:
Kong, X. Z., Huang, Y., Hao, X., Hu, S., & Liu, J. (2017). Sex-linked association between cortical scene selectivity and navigational ability. NeuroImage, 158, 397–405.

永久有效文章链接 | 未订阅数据库可访问公开链接(9月7日前有效)

这篇文章延续了我以往空间能力的研究主题,重点关注空间导航和场景加工活动,以及二者之间关联的性别差异。文章要点如下:

  • 男性自我报告有更好的空间导航能力 Males reported better navigational ability than females.
  • 男性在两侧旁海马位置区PPA有更强的场景特异性 Males showed stronger cortical scene selectivity in the bilateral PPA.
  • 在男性中,较强的PPA场景特异性与更好的空间导航能力呈现正相关 Higher selectivity in the left PPA was related to better navigational ability in males.
  • 在空间导航上,女性和男性可能有着不同的神经基础 Females and males possessed different neural correlates of navigation.

空间导航能力的性别差异

接下来是“大事记”。

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Personally Identifiable Brains

The idea of Personally Identifiable Brain (PIB) has been in my mind for a long time. This was largely inspired by Poldrack’s MyConnectome Project. You can find the structural and functional imaging data of my own brain from here (updating). The newly-proposed Brain Imaging Data Structure (BIDS) was used for preparing the files.

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Structural and functional MRI brain scans of (young) ME

It has been a long time since I planed to share the imaging data of my own brain. The idea is inspired by Poldrack’s MyConnectome project. As a neuroscientist, we usually scan our own brains. Although each single dataset is much smaller (compared to MyConnetome), many a little make a mickle. If these datasets are collected and shared, it would be a unique resource for better understanding of human brain, in particular of the neuroscientists’ brain and their academic life (as well as many other individual differences).

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海马之所以叫海马

海马(Hippocampus)是人脑中的重要结构,在大脑两侧各有一个,位于颞叶内侧区域。研究表明,海马主要负责学习与记忆,比如短时记忆信息的巩固和空间导航中的空间记忆等,因此,该脑结构的损伤会导致短时记忆缺失和迷失方向等症状,与阿尔兹海默症(Alzheimer’s disease)之间存在密切关联。
Hippocampus and seahorse
那么,为什么人脑中一个重要结构为什么叫“海马”呢?

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Parcellation display with the same color using freesurfer

Two methods for displaying ROI analysis results with brain parcellation in FreeSurfer.

  1. Solution #1 using R. The R code can be found HERE. After running the code, a configration file (like THIS) can be obtained. Then, by following the instructions at the end of the R code, you can have the display with tksurfer.
    surf vis 1

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WGCNA Background

WGCNA是Weighted Gene Co-expression Network Analysis的简称,其从网络连接的角度出发,考查基因之间的交互。该方法的提出背景是通过微阵列(microarray)实验可以获取的信息远多于仅得到一组差异表达的基因(differentially expressed genes)。基于微阵列microarray数据,我们可以通过计算基因表达模式(gene expression profiles)之间的相关来考查不同基因之间的交互。采用WGCNA方法,可以从数千基因的表达水平数据中识别可能具有临床价值的基因模块(gene modules),并最终采用模块内连接(intramodular connectivity)和基因-特质相关(gene significance)来发现某些疾病通路的关键基因,用于进一步验证。

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3D Print Your Brain from MRI

Do you think it would be cool to have a 3D printed brain of yourself? With standard anatomical MRI scanning and some 3D surface reconstraction methods, you can make it. Here are some useful links for making this dream come true.

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An Excel problem in scatter plot and solutions

Can you imagine using Excel without plot or formulas? Recently I came this kind of problem when using the Excel 2016 on my office PC: Excel functions like SUM() did not work, and I could not get any plot as expected. A bunch of questions flash across my mind. Is it a bug of the new version of Excel? Is my Excel corrupt or is this due to some malicious virus? This might also be caused by the different language using in the system. After a few days’ worry and search, here is the solutions to the problem I had, which might be helpful for others.

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Switching from Octopress to Hexo

Now, I am a reseach staff at a new institute. New campus, new air, new office, new computer. Everything is completelt new to me. To go on with my blog, I decided to switch (from Octopress) to Hexo, which is ‘A fast, simple & powerful blog framework’. So, March on, soldier!

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