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RSS订阅原创 HRF step by step
Preprocessing: Masks: 1. Real 1.1 Gaussian HRF first level analysis linear reg (uncorrected,P<0.01) 1.1.1 Higher level -> Grouplevel mask 1.1.2 Mask transform back to native
2017-02-23 03:36:55
573
转载 beta 和 correlation 的关系
acceptedAssuming you're talking about a simple regression model Yi=α+βXi+εiestimated by least squares, we know from wikipedia that β^=cor(Yi,Xi)⋅SD(Yi)SD(Xi)Therefore the
2016-09-21 22:03:33
1897
原创 FreeSurfer
1.Brain volume aparcstats2table –subjects *h.aparc.stats(Freesurfer 文件夹下stats文件，注意文件名只能取这个，否则找不到文件)
2016-08-04 22:09:10
1260
原创 Install Softwares
BEaST*Done? Need to test. - minc库位置 /opt/minc-itk4/lib - beast-library-1.1位置 /opt/minc-itk4/share/beast-library-1.1Usage: 1. $ source /opt/minc-itk4/minc-toolkit-config.sh2. PATH=$PATH:/opt/minc-i
2016-06-07 05:46:17
807
原创 MRI scanner 连线说明和实验步骤
按键盒： 左手盒blue yellow对应1，2右手盒green red对应3，4triger T白色USB——按键蓝色网线——eye tracking 黑色耳机线黑色视频线
2016-06-03 04:00:30
1260
转载 MPI compile 设置 centos 7
需要使用openmpi的mpi.h文件才能成功compile，因此要安装openmpi：sudo yum install openmpi-devel将possum下makefile中加一行CXX=mpicxxMake a folder to build the source code in, for example ~/fslbuild Put the tar file into your
2016-05-25 03:36:44
2213
转载 C++ debug in Linux——GDB
I find GDB (Gnu DeBugger) to be the best tool for c/c++. It’s probably already installed on your system if you have gcc installed.To use it, make sure you compile your program with the -g flag:gcc -g m
2016-05-12 00:44:29
296
1原创 Machine learning- PCA and ICA
两者都是一种坐标变换，假设原坐标系为x,y，新坐标系为z,w。 z=a1x+b1yz=a_1 x+b_1 y w=a2x+b2yw=a_2 x+ b_2 y - PCA 当x,y是两个独立高斯分布，两者正交(E[z,w]=0)和两者独立PZW(z,w)=PZ(z)PW(w)P_{ZW}(z,w)=P_Z(z) P_W(w)是等价的。如果在这种情况下使用ICA，其结果会收敛到PCA的结
2015-12-09 01:01:32
402
原创 Functional MRI (second edition) -- 10. Statistical Analysis：Basic Analyses
t-testt=x¯−y¯σxy=x¯−y¯σ2x+σ2y√t=\frac{\bar{x}-\bar{y}}{\sigma_{xy}}=\frac{\bar{x}-\bar{y}}{\sqrt{\sigma_{x}^{2}+\sigma_{y}^{2}}} 把该值换算成probability，需要除以自由度，自由度的计算方法是数据数n-1.如果数据集x中有p个数据，y中有q个数据，则自由度为p+q
2015-08-26 22:14:38
502
原创 Functional MRI (second edition) -- 9. Experimental Design
变量：分类方法1：Independent variables 自变量Dependent variables 因变量分类方法2：categorical variable 分类变量continues variables 连续变量控制量分配种类：between-subjects：将控制量放在不同的对象上。within-subjects：将控制量放在同一组对象上，一般比较推荐这种方式。Hyp
2015-08-21 20:16:55
275
原创 Functional MRI (second edition) -- 8. Signal, Noise, and Preprocessing of fMRI Data
Experimental Design 分为：blocked designs: 用于detection，即确定task激活的区域event-related designs: 用于estimation，即确定时间上的变化Analysis分为：voxelwise analysisregion-of-analysis(ROI) analysis
2015-08-07 10:32:26
435
原创 R -- 3 Installing R Packages
一般的R packages 都在CRAN，有些生医工相关的package在Bioconductor Project。a <- available.packages() ##查看一些package的相关信息head(rownames(a),3) ## Show the names of the first few packages会显示：## [1] "A3" "abc" "abcdeFBA"———
2015-07-30 21:18:38
659
原创 Markdown
Headings(会显示为标题)## This is a secondary heading### This is a tertiary headingUnordered List* first item in list* second item in list* third item in list
2015-07-30 21:07:05
243
原创 GitHub
git 常用 config命令$ git config -global user.name "Your Name Here"$ git config -global user.email "[email protected]"$ git config -list$ exit
2015-07-30 20:48:38
268
原创 Functional MRI (second edition) -- 7. BOLD fMRI: Origins and Properties
Ocygenated heoglobin(Hb) 富氧血红蛋白是diamagnetic反磁性的，使transverse方向的decay减慢，T∗2T_{2}^{*}变长，MRI信号变强。 ————————————————————————————– PET成像过程：radioactive tracer decay的过程中释放positron，与电子碰撞后释放gamma射线，通过接受gamma射线，
2015-07-26 10:27:09
361
原创 Functional MRI (second edition) -- 6. From Neuronal to Hemodynamic Activity
EPSP(excitatory post-synaptic potential) -
2015-07-23 15:35:43
340
原创 R -- 2. 简单函数Overview
ex: readLines()con <- url("http://www.jhsph.edu", "r")x <- readLines(con)ex: lapply>lapplyfunction (X, FUN, ...){ FUN <- match.fun(FUN) if(!is.vector(X)||is.object(X)) X<-as.list(X)
2015-07-16 20:45:29
382
原创 R -- 1. 如何查看函数
Access help file ？rnormSearch help files help.search(“rnorm”)Get arguments args(“rnorm”) 会显示：function （n, mean = 0, sd = 1） NULLSee code rnorm 会显示：function （n, mean = 0, sd = 1） .Externa
2015-07-16 20:29:51
367
原创 Functional MRI (second edition) -- 5. MR Contrast Mechanisms and Pulse Sequences
B增强时，T1T_{1} 变大，T2和T∗2T_{2}和T_{2}^{*} 变小。方便记忆可以思考陀螺的例子: - 当地球引力变大的时候，high-energy和low-energy状态之间的能量差变大，这时想改变状态就会变得更困难，因此T1T_{1} 变大。 - 同时为了保持平衡陀螺需要旋转的更快，因此相互间的相位更容易变得混乱，因此T2和T∗2T_{2}和T_{2}^{*} 变小。
2015-07-14 11:14:52
412
原创 Functional MRI (second edition) -- 4. Basic Principles of MR Image Formation
Bloch Equation dM⃗ dt=γM⃗ ×B⃗ +1T1(M0−Mz→→)−1T2(Mx→+My→)\frac{d\vec{M}}{dt}=\gamma \vec{M} \times \vec{B}+\frac{1}{T_{1}}(\vec{M_{0}-\vec{M_{z}}})-\frac{1}{T_{2}}(\vec{M_{x}}+\vec{M_{y}})————————–1 可
2015-07-10 14:44:14
330
原创 Functional MRI (second edition) -- 3. Basic Principles of MR Signal Generation(II)
公式解释：Magnetci Moment μ\mu: 在磁场中所受最大力和B的比。 Angular Momentum J=mωr2J=m\omega r^{2}———————1 gyromagnetic ratio γ=μJ\gamma=\frac{\mu}{J}————-2ex: 以单个质子为例 μ=IA=qTπr2\mu=IA=\frac{q}{T}\pi r^{2}———————————
2015-07-03 08:43:41
453
原创 Functional MRI (second edition) -- 2. MRI Scanners
M–main static magnetic field R –delivery of energy at the resonance frequency of the targeted atomic nuclei I – image formation ———————————————————————————————-
2015-06-21 01:03:52
403
原创 Statistical Analysis of fMRI Data- 2: Basic MR Physics
longitudinal relaxation: T1, spin return to parallel state (63%)transverse Relaxation: T2, loss of phase coherence (37%)TR: how often we excite the nucleiTE: how soon after excitation we begin data
2015-06-17 04:49:47
752
原创 Functional MRI (second edition) -- 1. An introduction to fMRI
phrenologists(颅相学家)：认为可以凭借颅骨的突出和凹陷来判断脑的每个功能区域的发育是否发达。position emission tomography(PET) 与 BOLD 的区别：PET需要注射造影剂，测量的是葡萄糖；BOLD测量的是血氧，不需要造影剂。———————————————————————————————————Measurement VS. manipulation
2015-06-14 23:32:43
454
原创 E-prime debug
没有SRBOX怎么办？ SRBOX是常用的一种键盒，如果没有SRBOX，在E-prime中会报错无法找到设备。这时只需要双击”Experiment”名，进入”properties”，在里面选择”device”页，将SRBOX前的勾选去掉。就不会再报错了。我们实验室使用的键盒的四个键分别对应键盘上的“rgyb”。如何改键？ 一般只需要在Initializeparameters文件里面进行编
2015-06-11 04:18:09
1070
原创 MRI task-base Experiment
Task setting:training 6min baseline test: 看到红色物体出现就按空格，用于测试被试的反应速度。（test用synscope写成）大约20min (2 blocks * 100 trials/block)： · screen1： 出现三个曲线形状。 · screen2： 出现一个曲线形状，判断该曲线是否在screen1上出现过。（test用E-pri
2015-06-06 05:06:21
404
原创 BOLD信号产生原理
专业词汇：BOLD: blood oxygenation level dependentCBF: cerebral blood flowE: cerebral oxygen extraction fractionCBV: cerebralblood volumeHb: hemoglobin(血红蛋白)CMRO2: cerebral metabolic rate of oxygenHb富氧
2015-06-06 04:48:43
3372
翻译 Global Linear Model
fMRI=β0+β1∗BOLD+errorfMRI=\beta_{0}+\beta_{1}*BOLD+error 即Y=Xβ+ϵY=X\beta+\epsilon minϵmin\quad\epsilon会得到β^=(XtX)−1XtY\hat{\beta}=(X^{t}X)^{-1}X^{t}Y因为ϵ−N(0,δ2I)\epsilon - N(0,\delta^{2}I) 推出 Y−N(X
2015-06-05 05:31:35
579
转载 bash shell 常用特殊字符
转自百度文库http://wenku.baidu.com/link?url=B6FJVno29INgmkxv3HpwLXQhLkS-qhDsIdFRVt1029jwlVPuMkJHd_CIAbQOHhMqlx5nfuulomdK2pjbQdGhyRGCLQm3Jci6zDgQEaB8ega在Bash shell中经常会见到一些比较特殊的符号，本人现收集与此，以供查阅：位置参数：
2015-06-04 02:34:26
257
原创 bash 6-10
Lesson 6： If statement #!/bin/bash MYNUM=100 if [ $MYNUM -eq 200 ] then echo “MYNUM is equal to 200.” else echo ” MYNUM is not equal to 200” fi
2015-06-04 02:26:12
292
转载 GSReg_demo
#!/bin/tcsh -fset sdir = $PWDset stat = 0set pname = `basename $0`SETUP: set gngain = 4.0 #base nz gain factor set gnr = (1.0 2.0 1.0 2.0) #nz gain factor per group, 30 subjects per group
2015-06-01 22:26:11
758
原创 Python 8 - Rock-paper-scissors-lizard-spock
Scissor > paperPaper > rockrock> lizardlizard > spockspock > scissorscissors > lizardlizard > paperpaper > spockspock > rockrock > scissors0-rock1-spock2-paper3-lizard4
2015-06-01 05:14:26
536
原创 Python 6 - Conditionals
def greet(friend, money) if friend and (money > 20): print "Hi !" money= money -20 elif frined: #else if print "Hi !" else: print "Ha ha"
2015-06-01 04:35:12
318
原创 Python 5 -Logic
True (T)False (F)NOT AND OR-------------------------------------------------------------------------------------------------------------------------------------------------------------a=True
2015-06-01 04:25:17
473
原创 Python 4- more operations
# Remainder - modular arithmetic# systematically restrict computation to a range# long division - divide by a number, we get a quotient plus a remainder# quotient is integer division //, the r
2015-06-01 03:55:03
346
原创 Python 3 -Functions
# computes the area of a triangledef triangle_area(base, height): # header - ends in colon，以冒号结尾 area = (1.0 / 2) * base * height # body - all of body is indented，body必须要退格 return area
2015-05-31 04:12:03
287
原创 Bash 14-16
Lesson 14： Sending Email with sendEmail sudo apt-get install sendEmail libio-socket-ssl-perl libnet-ssleay-perl #安装一些工具包 sendEmail -f [email protected] -t [email protected] -u This is ju
2015-05-29 02:19:02
313
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