Some tips to use wavelet toolbox

June 13th, 2016

Wavelet toolbox is a useful tool to study hyperscanning data. Many recent publications on NIRS hyperscanning use wavelet coherence to quantify the relationship between two interacting brains (e.g. Baker et al 2016, Nozawa et al 2016). You can see more information about wavelet coherence at http://www.alivelearn.net/?p=1169

wavelet

wavelet

Here are some tips to use the toolbox:

1. It often takes a long time to run Monte Carlo simulation. You may use ‘mcc’=0 to disable it.

figure;wtc(signal(:,jj),signal(:,jj+22),'mcc',0);

2. If you need to get the values of the result (instead of the graphic), you may specify the return value

[Rsq,period,scale,coi,sig95] = wtc(signal1,signal2,'mcc',0); %Rsq is a complex matrix

3. If you are only interested in a certain band, you can specify the MaxScale (i.e. ms) parameter. More information at http://www.alivelearn.net/?p=1518

[Rsq,period,scale,coi,sig95] = wtc(signal1,signal2,'mcc',0, 'ms', 128);

4. If you are interested in finding the “phase” information (visualized by the arrows), you may use xwt function. The returned value is a complex matrix and you can calculate the phase.

[Rsq,period,scale,coi,sig95] = xwt(signal(:,jj),signal(:,jj+22));
figure;imagesc(angle(Rsq));

5. To visualize the power of a single signal, you may use wt, which I personally feel much better than FFT.

figure;wt(signal(:,jj));

6. To change the density of the arrows, you may specify the ArrowDensity parameter

figure;wtc(signal(:,jj),signal(:,jj+22),'mcc',0,'ArrowDensity',[30 30]);

Do you have any tips? Please let me know.

Author: Xu Cui Categories: brain, matlab, nirs, programming Tags:

Just published a paper: Men vs Women, are they different in cooperation?

June 13th, 2016

We just published a big and long study. It is a NIRS hyperscanning study aiming to investigate the brain difference between men and women during cooperation. We have scanned 222 people! And it is one of the largest NIRS study I have seen. And it is a long study. The project started in 2012 (today is 2016/6/13). You can imagine how long it took to collect and analyze the data, and to get the paper published!

After a series of rejections (Nature -> Journal of Neuroscience -> PNAS -> NeuroImage), this paper was finally published in Scientific Reports this month (2016/06). The full-text of this paper is accessible via PubMed Central.

A cooperation game

Two lab members are playing the cooperation game

After the paper was published, it has attracted a lot of media attention. For example, Stanford news center has reported “Study finds differences in male, female brain activity when it comes to cooperation” (below).

Stanford News Center

Stanford News Center

Two major contributors of this study are Ning Liu and Joe Baker.

Ning Liu

Ning Liu

Joe Baker

Joe Baker

Author: Xu Cui Categories: brain, nirs Tags:

Hitachi ETG4000 on ebay, for less than $10,000

June 6th, 2016

In our lab meeting today we accidentally discovered that you can actually purchase a used ETG4000 on ebay! The seller asked for $9,995. When we purchased ETG4000 back in 2007, it costed us about half million!

Check it out:

http://www.ebay.com/itm/Hitachi-Medical-ETG-4000-Optical-Topography-System-Cerebral-Cortex-Imaging-/262352769323?hash=item3d1571912b:g:UjMAAOSwGYVW9WqW

Author: Xu Cui Categories: brain, nirs Tags:

fNIRS 2016

June 6th, 2016

fNIRS 2016 conference will be held in Paris, October 13 – 16, Université Paris Descartes, 12 rue de l’Ecole de Médecine, Paris 75006, FRANCE

Check out the society’s home page: http://www.fnirs2016.org/

The 2016 conference will take place in central Paris, October 13 – 16, 2016.

As with past meetings, there will be a day-long course prior to the start of the conference, on Thursday, October 13.

The conference is co-chaired by Judit Gervain and Joseph Culver.

INVITED SPEAKERS
Maria Angela Franceschini (MGH, Harvard Medical School, Boston, USA) – Keynote
Sol Diamond (Dartmouth College, USA)
Frédéric Dehais (ISAE, Toulouse, France)
Ursula Wolf (Bern University, Switzerland)
Frédéric Lesage (McGill University, Canada)
Gorm Greisen (University of Copenhagen, Danemark)
Yasuyo Minagawa (Keio University, Japan)
Ippeita Dan (Jichi Med. University, Japan)
Chuck Nelson (BCH, Harvard Medical School, Boston, USA)

IMPORTANT DATES
Abstract submission opens: May 1st, 2016
Abstract submission ends: June 10th, 2016 (midnight GMT)
Notification to authors: Late July 2016
Early registration ends: Sept 10th, 2016

Author: Xu Cui Categories: nirs Tags:

DDoS Attack Threat

May 26th, 2016

I recently received an email who threatens to attack a server I am running - unless I pay them 0.2 Bitcoin (about $93 US dollars). Anybody know how to handle this?

Below is the email:

—–

From: PhantomSquad@openmailbox.org
subject line: DDoS Attack Imminent - Important information

FORWARD THIS MAIL TO WHOEVER IS IMPORTANT IN YOUR COMPANY AND CAN MAKE DECISION!

We are Phantom Squad
http://lmgtfy.com/?q=Phantom+Squad

Your network will be DDoS-ed starting June 1st 2016 if you don’t pay protection fee - 0.2 Bitcoin @ 14hxG5TBZz6jCZz4H7mzfzXfgXjgaF3MqA.

If you don’t pay by June 1st 2016, attack will start, yours service going down permanently price to stop will increase to 20 BTC and will go up 10 BTC for every day of attack.

This is not a joke.

Our attacks are extremely powerful - sometimes over 1 Tbps per second. And we pass CloudFlare and others remote protections! So, no cheap protection will help.

Prevent it all with just 0.2 BTC @ 14hxG5TBZz6jCZz4H7mzfzXfgXjgaF3MqA

Do not reply, we will not read. Pay and we will know its you. AND YOU WILL NEVER AGAIN HEAR FROM US!

Bitcoin is anonymous, nobody will ever know you cooperated.

Author: Xu Cui Categories: web Tags:

Who cited my paper?

May 9th, 2016

Back in 2010 we published a paper titled “Functional Near Infrared Spectroscopy (NIRS) signal improvement based on negative correlation between oxygenated and deoxygenated hemoglobin dynamics“. It is about a really simple method which surprisingly works well in reducing motion artifact (noise) in NIRS data. As of today (2016-05-09), the paper has been cited by more than 130 times.

Who cited this paper? Well, we created this map to show where the authors are:

If you clicks the red dots you will find the detailed information about the paper, such as the author name and journal.

Then who are the top researchers who cited this paper? We count the number of citation for each author, and rank them by the number of papers. Here are the top authors who cited our 2010 paper:

Author Number of Papers
Fallgatter, AJ 9
Ehlis, AC 8
Hong, KS 8
Dresler, T 8
Herrmann, MJ 7
Scheutz, M 6
Strait, M 5
Boas, DA 5
Sato, H 4
Scholkmann, F 4
Herff, C 4
Seghouane, AK 4
Ge, SS 4
Shah, A 4
Katura, T 4
Molavi, B 4
Wolf, M 4
Author: Xu Cui Categories: brain, nirs, programming Tags:

NIRS manufactures locations

May 4th, 2016

Where are the major NIRS device manufactures? You can see from the map below.

There are NIRS manufactures in US, Japan, Europe and Korea.

If you are a NIRS manufacture and would like to add to this list, please let me know (leave a comment in this post).
If you are interested in creating a map like this, please let me know (leave a comment in this post).

Related: NIRS manufactures products http://www.alivelearn.net/?p=1335

Author: Xu Cui Categories: brain, nirs Tags:

Stork is my best research assistant (2): Grant alert

April 15th, 2016
  1. Does my boss have money?
  2. I am looking for a postdoc position; does my future boss have enough funding to support me?
  3. How much money was awarded to my field (e.g. NIRS)? And who got the money? What are they going to do with the money?

Have you ever wondered these questions? In the early years as a graduate students, I rarely asked “money” questions. It does not sound what a “true” scientist should care.  I was even puzzled when I realized my boss spent more than half of his time writing grant applications - shouldn’t he spend most of his time doing experiments and write papers?

As a postdoc I found myself spend a lot of time writing grant applications; and realized my career is critically depending on the success of securing enough funding. I also see a few colleagues had to leave academia due to lack of funding.  It would be nice if there is a tool which can notify me of the funding situation in a timely manner.

Stork is such a tool.

I entered some keywords into Stork, including “pearl chiu” (my former colleague) and “nirs brain” (my research field). Below is a letter I got from Stork:

Stork notifies me of awarded grants

Stork notifies me of awarded grants

With the information Stork provides, I know who in our field got grants and what they proposed. In fact the 3rd one is my colleague Manish who is interested in using NIRS in resting-state brain network study. I also got to know Pearl got a big gran, so I sent her a congratulation note.

Compared to journal papers alert, grants alert helps me to know the trend of my field much earlier. This is because publications are usually a few years delayed from grants.

If you also want to be the first one to know new grants in your field, why don’t you give Stork a try? I’m sure you’ll be delighted!

Author: Xu Cui Categories: brain, life, programming, web, writing Tags:

Projection of a NIRS channel on a brain surface

April 11th, 2016

When analyzing the data in our concurrent NIRS-fMRI study, we are particularly interested in how the NIRS signals were correlated to the fMRI signal. To answer the question we need to create an ROI (region of interest) in brain which is directly underneath the NIRS channel (which is on the skull). So a projection of the NIRS channel on the brain surface is necessary.

It might be easy if the brain were a perfect sphere, or at least doable if it is smooth. But brain surface is anything but smooth. What we did is:

  1. Create a brain surface mask. This is easy using BET (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET)
  2. Loop over all voxels on the surface, calculate the distance between the NIRS channel (point A) and the voxel
  3. Find the voxel which is closest to the NIRS channel (It is point B in the figure below)

Projection of NIRS channel on brain surface

Projection of NIRS channel on brain surface

Author: Xu Cui Categories: brain, matlab, nirs, programming Tags:

Is measuring both oxy and deoxy-Hb useful?

March 28th, 2016

One of the advantages of NIRS is that it measure two values at a time - both oxy- and deoxy-Hb concentration, while fMRI measure only one value, called BOLD. (See a comparison between NIRS and fMRI.) However, what is the use of measuring two values if they are highly correlated (actually anti-correlated)?

This is a valid question. In our 2010 paper titled “Functional Near Infrared Spectroscopy (NIRS) signal improvement based on negative correlation between oxygenated and deoxygenated hemoglobin dynamics“, we have shown that (1) theoretically (using Balloon model) oxy and deoxy Hb should be highly correlated, close to -1; (2) with real data, they are highly correlated. See the figure below with real data (I was the subject).

oxy and deoxy-Hb are highly (anti)correlated

oxy and deoxy-Hb are highly (anti)correlated

Now go back to our question: if they are highly correlated, maybe measuring both does not bring additional advantage. If we look at NIRS publications, we see most publications only use either oxy-Hb or deoxy-Hb in their analysis, or at least use them separately. It is not very clear why we should use both.

However, it turns out it is an advantage to measure both. In a study we have tried to “predict” if the subject is doing finger tapping or not by looking at the NIRS signal only (see the paper). This is useful for brain-computer-interface purpose. In the figure below, you will see that if we use only oxy-Hb (blue) or deoxy-Hb (green), the prediction accuracy is lower than if we combine them (red).

Combined oxy- and deoxy-Hb predict better

Combined oxy- and deoxy-Hb predict better

This means while oxy- and deoxy-Hb are highly correlated, we still get more if we measure both. I think part of the reason is that there are always noise in real data. With two measurement the signals are more robust again the corruption of noise.

Author: Xu Cui Categories: brain, nirs Tags: