Xu Cui

Download the following 4 files:

1. porttalk.sys, copy to C:\WINDOWS\system32\drivers
2. lptread.m
3. lptread.mexw32
4. lptwrite.mexw32

Copy the last three files to a directory where your matlab can access.

Your LPT port number is probably 0×378 (or 888). Assume lptport is the port number, then we use lptread to read from the port:

val = lptread(lptport)

and use lptwrite to write to the port

lptwrite(lptport, val)

As a real example, we want to control the step motor Gary created to investigate motion artifact in fMRI. Here is a sample code:

lptport = hex2dec('378');
dir = hex2dec('40');
data = hex2dec('20');
for ii=1:30
    lptwrite(lptport, data+dir);
    pause(0.005)
    lptwrite(lptport, dir)
    pause(0.005)
end

I wrote some batch scripts for NIRS-SPM. They, together with NIRS-SPM and xTopo, are called “super” package (I apparently run out of names). The “super” package are located in directory:

/fs/quarry/cuixu/NIRS/super

Please don’t modify the files inside.

“super” contains the following scripts:

1. mes2NIRSSPM, which converts Hitachi measurement data (in csv format) to NIRS-SPM recognized format (.mat file). Note: this script allows you to convert one or two files (for bilateral 3×5 and 4×4 configurations, you have 2 csv files) into one mat files. NIRS-SPM itself only convert 1 (I already contacted NIRS SPM developers to add this functionality.).
2. spec, which specify your general linear model (design matrix), including data file, where to save spm files, either HbR or HbO, onset timing, duration etc.
3. estimate_indiv, do estimation
4. cuixu_nirsContrast, do contrast. Here you specify contrast vector etc
5. estimate_group, do group estimation

All of these scripts can run alone — you don’t need to click button etc. To get more information of how to use these scripts, you may type help <script name>.

Here is instructions:

1. Log in to server (e.g.  ssh fmri@scuttlebutt -Y)
2. Start matlab with SPM5 in the path (e.g. ml7spm5 -jvm)
3. add the path of super
   addpath(genpath('/fs/quarry/cuixu/NIRS/super'))
4. Enter a directory where you prefer to work (e.g. your data’s directory).
5. Use mes2NIRSSPM to convert csv to mat file. e.g.
   mes2NIRSSPM(nirsfile, ['converted_NIRS_' subject_name])
   Note: nirsfile is a cell array. Each element is a file name. For 4×4 and 3×5 configurations, you have 2 files; for 3×11, you have only one.
6. You need to configure your channel positions and get a channel position mat file. You can use the default files provided in super/templateFile/.
7. use spec to specify design matrix. e.g.
   spec(’converted_NIRS_c.mat’, ‘./newspmdir’,1, {’trial1′,’t2′},{[1:1:100]‘,[2:2:200]‘},{ones(100,1),ones(100,1)*2});
   Type help spec for more info.
8. use estimate_indiv to begin estimation. e.g.
   estimate_indiv(spmfile)
9. use cuixu_nirsContrast to do contrast.
10. Repeat step 5-9 for other subjects
11. use estimate_group to do group analysis
12. To view result, launch nirs spm, click button “Results NIRS”. There you input the individual (or group)’s spm file, and channel location mat file (not required for group), and click button “Contrast”.

Leave a comment here if you have a question.

因为写peaya paper的缘故，对Adobe的一些新技术有所了解，简单介绍几个吧：

1。stratus，rtmfp服务器，可以实现p2p网络电话，视频聊天。也可以做简单的游戏。现为beta，免费，不清楚以后是不是收费

http://labs.adobe.com/technologies/stratus/samples/#resources
http://labs.adobe.com/technologies/stratus/

2。Adobe Flash Collaboration Service，比stratus更强大些，可以多人聊天，聊天室，黑板，文件传输分享等。beta

http://labs.adobe.com/technologies/afcs/

3。Alchemy，可以让C C++代码编译成可在flash或AIR下运行，速度和C接近。我自己没有多实验，不过听起来很不错，因为flash给人的感觉就是比较慢,这样会快很多。

http://labs.adobe.com/technologies/alchemy/

http://www.newgrounds.com/portal/view/470460
http://www.unitzeroone.com/labs/alchemyPushingPixels/
http://www.peternitsch.net/ascii/pv.html

4。catalyst，可以在photoshop里画程序界面，然后转换成真正的界面。

http://labs.adobe.com/technologies/flashcatalyst/

5。Adobe AIR，不算新了（有两年了），可以用web程序语言（ajax,actionscript)写跨平台独立的桌面程序。peaya paper就是基于actionscript和AIR

http://www.adobe.com/products/air/

话说当年孙悟空大闹天宫，观世音菩萨举荐二郎神带兵降妖，天兵天将在花果山群猴大战。正斗间，大圣忽见本营中妖猴惊散，自觉心慌，抽身就走，众天将慌慌张张，前后寻觅不见，一齐吆喝道：“走了这猴精也！走了这猴精也！”

二郎神圆睁天目观看，却见下界人烟繁华之处，那大圣变做一个老头，推着一辆三轮车，抖抖索索地，正在街边卖烤白薯。二郎心中冷笑，正待发标打他，忽然见 一伙城管，手持锤剪棍棒，吆吆喝喝，不由分说，便将三轮车砸得稀烂。大圣一惊，以为是天兵到来，连忙转过街角，又摇身一变，变做一个小姐，描眉画眼，在那 里袅袅婷婷走路。却又被二郎看个真切，二度意欲发标，迎面却又来了几个公安，劈面揪住大圣道：“定是一个野鸡，随我局子里走一趟！”大圣心慌，忙道：“我 不是野鸡，我还是处女！”公安狂笑道：“处女怎地？处女便不能卖淫么？”手铐一抖，便要拿人。大圣见事不谐，忙将腰一扭，腾空而去，眼见前方一个山凹，便 滚下山崖，伏在那里又变，变一座小学，大张着口，似个校门，牙齿变做门扇，眼睛变做窗棂，抖几个猴虱下来变做学生咿咿呀呀念书。只有尾巴不好收拾，竖在后 面，变做一根旗竿，悬起一条大标语：“百年大计，教育为本；义务教育，免费入学。”二郎两番被抢了先手，心中正在烦闷，眼看得这条标语，不由笑道：“是这 猢狲了！他今又在那里哄我。殊不知中国号称义务教育，那里有得免费？我也曾见过学校千万，更不见一个不把学生做摇钱树的，看我打杀这个猴子！”大圣听得心 惊，扑的一个虎跳，又冒在空中不见。

二郎神望不见大圣踪影，急纵身驾云，起在半空。见那李天王高举望远镜站在云端，呵呵笑道：”二郎神,快去！快去！那猴使了个隐身法，走出营围，往你那灌江口去也。”二郎听说，忙回灌江口来赶。

却说灌江口正开大会，大圣摇身一变，变做一个XX代表，杂在会场之中，指东点西，做踊跃发言状。正自以为得计，却不料被真君一眼识破：“XX代表向来是 泥塑土偶的神像，什么时候跑出一个活的来？”举着三尖两刃神锋，劈脸就砍。那猴王急忙躲过，使金箍棒相对。两个嚷嚷闹闹，打出会场，半雾半云，且行且战。

半空中天庭妇联主任观音菩萨与炼丹部长太上老君正在观战。菩萨对老君道：“老君哥哥，贫僧所举二郎神如何？果有神通，已经把 那大圣围困，只是未得擒拿。我如今助他一功，拿下猴头。”老君道：“观音妹子？你将何兵器助他？”观音回身唤过坐骑：“看我开宝马撞他一下。”老君道：“ 你那宝马价格甚为昂贵，若撞坏了多有不便。”观音道：“横竖也是公款，撞了就撞了吧。”老君又道：“那修理起来也甚为麻烦，还是让我来替妹子助他吧。”观 音曰：“坏了就不要了，我正想换辆凯迪拉客。”正拉拉扯扯间，老君身后转过一名仙娥，乃是有名的张惟英教授，献与老君一件宝物，嘴里喃喃说着什么 “总不能让所有人都来天庭吧……我至今都不认为我错了……”转身而去。老君定睛看时，那宝物却是一件“天庭人口准入制度”，不由大喜：“此物一出，凡间九 亿农民都得发抖.正可用来对付山野村猴，等我丢下去打他一下。

只见老君将那法宝自天门上往下一掼，滴溜溜，可可砸着猴王 头上一下，将大圣打翻在地，众天庭公安一拥而上，将大圣捆个结实，再也不能变化。一公安怒道：“这厮令我等吃了不少苦头，今日一发还了他罢！饶你个孙悟 空，今日要将你变做第二个孙志刚！”正待把出手段，却有另一公安叫道：“且慢，我等老手段土得掉渣，如今时兴与国际接轨，那驻伊美军虐囚，手段千变万化， 何不学得一二，今日做个新鲜耍子？”众公安一听，齐声称妙，便将大圣押去斩妖台，电击火烧，刀砍斧剁，却伤不得大圣分毫。

玉帝见状，不由踌躇：“这厮这等，这等……如何处治？”老君奏道：“不若与老君领去，放在八卦炉中，炼出我的丹来，何如？”玉帝闻听大喜，便将大圣赐与 老君锻炼。殊不知大圣神通广大，拔下一根毫毛，变做美钞，贿赂了扇火童子，得知那巽位下有风无火，前往躲避，未曾受得重伤。

七七四十九日满，老君开炉取丹，却见大圣飞身而出，使金箍棒大杀四方，打得天宫中九曜星闭门闭户，四天王无影无踪。直打到通明殿前，玉帝见状大惊，忙叫 道：“快，关门，放协警！”原来那协警之徒，比正规警察更凶恶十倍，只见一个个奋勇争先，踊跃咆哮，将大圣围在垓心，眼看就要拿下。

玉帝正在庆幸，忽见协警们全做了鸟兽散，原来此辈性贪，眼中只有金银，大圣之黄金锁子甲在炉子中烤得甲环松脱，被众协警一口一撕，顷刻间个个嘴里有片黄金，纷纷跑回后院掩埋收藏不提。

正没奈何间，忽见西方如来相助，要与大圣赌赛。如来曰：“我有一样法宝，你若能飞出我这法宝管辖，便让你做了玉帝之位；若飞不出，便缴械投降如何？”说 罢自怀中掏出法宝，悟空定睛看时，却是一个小小本子，上书三个大字：暂住证。便笑道：“一个小小本子，有何灵能，我去也！”一个跟头飞出，自天空降落北京 地界，脚步刚落，便见几名警察前来：“那个谁，说你呢！暂住证拿出来看看！”悟空一惊，将腰一扭，又一个跟头飞到广州，正在观望，忽见一群联防冲来：“这 个好像没有暂住证，快抓住他！”七手八脚要拿下大圣，大圣忙分开众手，复又飞起，急切间难辨方向，却又飞回如来面前。如来微笑道：“我的宝贝何如？”大圣 道：“不算！不算！闻听西方有国，不设暂住证，待我去来！”正要纵身跳出，却被如来手掌一翻，将暂住证变做一座五行山，将大圣牢牢压住。

玉帝见擒了大圣，心中大喜，便邀请如来及有功群臣，开了一个庆功大会，盛世联欢。正行乐间，忽有五行山居委会老太来报：“那大圣伸出头来了，说他要挣脱 出去赶招聘会，投简历发名片，谋个职位，以图东山再起哩！”如来道：“不妨，不妨。”袖中只取出一张帖子，上有六个金字：“此人农村户口。”递与手下，让 贴在那五行山顶上。又向天再借五百年，使那帖子牢牢置顶不得脱落，那座山即生根合缝，大圣再也无法爬出，自此一压就是五百年不得翻身也。

10-20 system is a method to localize brain areas. It uses 4 landmarks of head:

1  the nasion which is the point between the forehead and the nose;
2  the inion which is the lowest point of the skull from the back of the head and is normally indicated by a prominent bump.
3  the preaurical point (left and right)

All other points are derived from these landmarks.

All points are denoted with a letter and a number. The letters F, T, C, P and O stand for Frontal, Temporal, Central, Parietal and Occipital respectively. Note that there exists no central lobe, the “C” letter is only used for identification purposes only. A “z” (zero) refers to an electrode placed on the midline. Even numbers (2,4,6,8) refer to electrode positions on the right hemisphere, whereas odd numbers (1,3,5,7) refer to those on the left hemisphere.

Even though I learned power analysis in elementary statistics class, I totally forget it because I never use it. As we have to put power analysis in our grant, I am forced to relearn this topic.

Definition: type II error:

• null hypothesis should be rejected but we don’t
• or, false negative (there is an effect but fail to detect it)

(Null hypothesis is usually boring, e.g. mean=0, or no difference between two samples etc. So null hypothesis usually means no effect, or negative. Rejecting null hypothesis is “finding positive effect” and thus usually “exciting”. )

Definition: the probability of type II error is called beta

Definition: power is 1 - beta

How to calculate beta (or power)?

You need (1) null hypothesis (2) alpha, type I error cut off, usually 0.05 (3) standard deviation (or distribution) of samples

Step:

1. calculate the decision point (to reject or accept null hypo) based on your null hypo and alpha
2. calculate beta based on the decision point above and (3)

Example:

You null hypothesis is “mean of A is 0″. You measured A 100 times. The mean is 1 and standard deviation is 10 (and thus the standard deviation of mean is 10/sqrt(100)=1). You are deciding if the null hypothesis should be rejected and what is beta if alpha is 0.05. You calculate and find the p value is 0.1587, which is bigger than 0.05 so you accept the null hypothsis.

Then what is the probability that this decision is indeed wrong (you accept null hypo but indeed null hypo is false)? or beta?

As you make decisions based on alpha = 0.05, that means your decision point of mean of sample is 1.65: if the mean of sample is bigger than 1.65, you reject null; if smaller than 1.65, you accept it (like in our case where mean is 1). So beta equals to the probability that you find mean of sample is <1.65, while the true mean is 1. And this probability is 0.74. And power is thus 0.26.

To increase power, you usually need to increase the sample size. In our case, as the standard deviation of sample is very high, we need a lot more samples. If our N = 400, then our decision point will become 0.83 and the power will increase to 0.63.

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