To beginner: task-based fNIRS study design (1)

March 10th, 2018

This is a guest post by Ning Liu from Stanford University.

For someone who has no imaging background and just began to use fNIRS, s/he might be surprised to find out that the imaging study design is so different with study designs in other fields. For instance, task-based imaging studies usually involve bunch of repeated stimuli. This is quite different with what we usually do in a naturalistic environment in our daily life. Why not use just one stimulus? This is due to the difficulty in detecting signal changes against a much stronger background physiological noise. Thus, in order to measure brain actives, one needs to carefully design the experiment and use some clever method to analysis the data.

For task-based study, there are two types of basic design. One is called block-design and the other event-design. It worth noticing that they have something in common — the same stimulus needs to be repeated many times, and the detected signal changes are statistically tested for significance.

Another aspect that beginners usually ignore is the design of control condition. A typical task design usually contains epochs or events of interest along with control epochs or events, such that a cognitive subtraction (for instance) can be performed and resulting in robust and reproducible results.

Author: Xu Cui Categories: brain, nirs Tags:


March 10th, 2018


对于一个近红外初学者,特别是没有任何脑成像背景的初学者,他们往往没有想到脑成像的实验设计和别的学科的实验设计,诸如行为科学或者生物实验等有很大不同。通过一些文献阅读或者相关培训,初学者可能注意到脑成像的任务态实验设计往往有很多重复的环节。那么,为什么脑成像的实验需要这样的设计?究其根本原因,其实是因为现有的无侵入式脑成像技术,无论是核磁共振脑功能成像(fMRI) 还是近红外脑功能成像(fNIRS), 其直接测量到的信号变化与噪音相比都太小(~1%量级)。换言之,巨大的生理噪音掩盖了信号的变化。因此,为了能测量到与大脑活动相关的信号,具体到近红外成像中就是测量到氧合血红蛋白和脱氧血红蛋白的浓度变化,就需要巧妙的设计实验和分析数据。

对于任务态实验,有两种基本的实验设计:一种是采用组块设计(block design),另一种是采用事件设计(event design)。然而,无论哪种,它们的共同点是:实验中多次重复同一个任务/操作,数据处理时通过建立模型,用统计的办法找出具有统计意义的相关活跃脑区。

任务态的实验设计中常常被初学者忽略的另一个重要环节就是对照条件(control condition)的设计。刺激任务除了设计能激活相关脑区的任务以外,一般还应该设计一个好的对照条件,进而可以通过两种条件下脑信号的对比,找出真正与任务相关的脑区。

Author: Xu Cui Categories: brain, nirs Tags:

近红外成像入门培训 —— 小型私人辅导

February 23rd, 2018


近红外成像入门培训 —— 小型私人辅导
专门针对初学者,不需要任何近红外成像经验和背景。 近红外专家用最浅显易懂
包括医生(精神科、儿科、脑外科 等)、大学本科生、研究生、以及高中生等,得
(1) 近红外脑功能成像技术原理及理论基础
(2) 数据采集基本流程
(3) 单人扫描实验设计及数据处理
(4) 双人同步扫描(超扫描)实验设计及数据处理
培训老师: 刘宁,生物医学工程博士(近红外成像方向),现任斯坦福大学助理
人群 脑功能成像。

Author: Xu Cui Categories: nirs Tags:

How to find NIRS experts using “Find Experts” app

January 12th, 2018

If you are a newcomer in the NIRS field, you may wonder who are the experts in this field. You might know a few already - for example your boss. But who else are there and where they are?

We developed “Find Experts” app to quickly find experts based on scientific publications in any biomedical field. Let’s see who are experts in the NIRS field.

Use "Find Experts" to find experts in NIRS field

Website: Find Experts of Stork

Author: Xu Cui Categories: programming, stork Tags:

Number of PubMed papers

December 7th, 2017

From 2000 and 2010, the number of PubMed citations had grown from half million to 1 million. Today we see ~3,000 new papers everyday!

PubMed citations doubles in 10 years

PubMed citations doubles in 10 years

Year Number
2016 1258608
2015 1253004
2014 1201621
2013 1146180
2012 1085504
2011 1017939
2010 940347
2009 875631
2008 835283
2007 784836
2006 746487
2005 699162
2004 638433
2003 593404
2002 564380
2001 546100
2000 531703
1999 492961
1998 473304
1997 455641
1996 457788
1995 448124
1994 437709
1993 426674
1992 417191
1991 412490
1990 410185
1989 402163
1988 386534
1987 367462
1986 349127
1985 334843
1984 317837
1983 309102
1982 295041
1981 283253
1980 280186
Author: Xu Cui Categories: writing Tags:

How to track new NIRS publications and grants?

October 27th, 2017

Near infrared spectroscopy (NIRS) is an increasingly popular technology in brain imaging research. Compared to fMRI, NIRS can be used for more naturalistic experiments, including face to face communication, natural body movements, sports, infants, and is well suited for real-time applications.

If we count the number of NIRS publications using keyword (NIRS OR fNIRS) AND brain, we find the number increases steadily over the past 10 years:

With this trend, it’s expected that we will reach a speed of 1 new paper every day in the year of 2018 or 2019. This is a fast field, and it’s nearly impossible for us to search (NIRS OR fNIRS) AND brain every day or even every week. For a student who does not follow literature proactively, he might know of a paper a year after its publication.

The easiest way to solve this problem is to use an app to notify us of the new publications. The one I use is called Stork . All I need to do is to enter a few keywords I am interested in, e.g.:


But what if I want to follow more specific fields, such as hyperscanning, or comparison with fMRI etc? We can enter the following keywords:
(NIRS OR fNIRS) AND brain AND hyperscanning
(NIRS OR fNIRS) AND brain AND "deep learning"
(NIRS OR fNIRS) AND brain AND social

What if I want to follow some scientists in the field? We may enter their names, such as:
David Boas
Allan Reiss (NIRS or fNIRS)

After we setup the keywords, Stork, like a diligent assistant, will search for us every day. If she finds something, she will send an email to us, listing the new publications. A recent example is shown below:

fmri nirs

The Temporal Muscle of the Head Can Cause Artifacts in Optical Imaging Studies with Functional Near-Infrared Spectroscopy. by Martin Schecklmann, Alexander Mann, …, Florian B Haeussinger (2017) Front Hum Neurosci (impact factor: 3.6) Free full text

nirs brain

Enhancing Performance of a Hybrid EEG-fNIRS System Using Channel Selection and Early Temporal Features. by Rihui Li, Thomas Potter, Weitian Huang, Yingchun Zhang (2017) Front Hum Neurosci (impact factor: 3.6)Free full text

Not only does Stork search scientific publications for you, she also searches NIH grant database (this is an advanced feature). That means whenever some researchers receive a grant on NIRS, you will know it. You will know what is his research direction in the next few years, how much money he received etc. This feature is mostly useful for professors and senior graduate students and postdocs.

The link of Stork is: and it’s very easy to use.



Author: Xu Cui Categories: nirs, stork Tags:

xjview 9.6 released

October 12th, 2017

In this version, we modified the templates for 3-D render view and use a high-resolution template. It also includes a few scalp view. You may pick up your favorite display for your paper (or presentation). Please go to the download page to download.

xjview 9.6 Render View xjview 9.6 Render View

The render view for the previous version is shown below to compare.

xjview 9 Render View xjview 9 Render View

This update is brought to you by Dr. Weiwei Men (email: wmen AT from Center for Magnetic Resonance Imaging Research, Peking University, China. Weiwei has been using xjView for 10 years. He noticed that the image resolution of the render view in xjView 9 is low, and took the effort to create a new view using a high resolution template (ICBM152_asys_2009C). Thank him for his excellent work!
Weiwei Men

Author: Xu Cui Categories: matlab, programming Tags:

How much do we know about the universe? Hubble’s Ultra Deep Field Experiment

September 13th, 2017

When we looked at the space at night, we see a lot of stars, dotted on a vast dark space. But is there anything in the dark area?

Guess, in the photo below, how many stars are in the red circle? None? A few? A few thousand? Billions of stars?

How many starts in the red circle?

How many starts in the red circle?

In 2002-2004, Hubble telescope zoomed in this region and found, in this seemingly empty space, there are not 10 stars, 1000 stars, but at least 3,000 galaxies each with hundreds of billions of stars!

There are 3 thousand galaxies with trillions of stars

There are 3 thousand galaxies with trillions of stars

What do we know about the universe?

Author: Xu Cui Categories: opinion, writing Tags:

What is reality?

September 9th, 2017

David Eagleman was my co-advisor during my Ph.D study in Baylor College of Medicine. He produced a documentary movie last year with BBS addressing an important question “What is reality?” based on advances in neuroscience. I personally find it eye-opening and provoke deeper thinking of our own existence.

Here is the video:

Author: Xu Cui Categories: brain Tags:

[Tool] How To Convert Image To Text (OCR)

September 9th, 2017

You are reading a book or article online, and want to copy/paste a few sentences. But then you realize the book or article prevents you to copy, or maybe the book/article is an image. Instead of typing the sentences, you can use a tool to automatically recognize texts in image and convert for you.

“structurise” is such a tool. Unlike other online tools, you can paste your image into structurise directly, instead of saving the image to a file and uploading it. So it really make your workflow fast:

A short demo recorded by myself (in Chinese)

Author: Xu Cui Categories: web, writing Tags: