Handy programs to visualize NIRS data (6): plotAverage

55 sec read

This is the 6th post of the series: Handy programs to visualize NIRS data

When we do an experiment, we often repeat an event (or block) for a few times. For example, in a typical finger tapping task, we ask the participants to do a finger tapping for 20s, then rest for 20s, then repeat the whole tap-rest paradigm for 10 time.

After we extract the NIRS time courses, we often need to know the average of the signal over all repetitions of the event. In the finger tapping experiment, we want to know the average signal across 10 blocks of finger tapping.

What we need to do is:

  1. Know the timing of each block (of course!)
  2. cut the NIRS signal into pieces. The starting points should be a few seconds before the onset timing of the experiment block; and the ending points should be a few seconds after the offset of the experiment block.
  3. Align the pieces and average
  4. Also calculate the standard deviation (or error) of the average
  5. plot
The attached cuixuNIRSretrieve.m and plotAverage can automatically do the above steps. Below is a plot done by plotAverage. In this example, there are two types of events, fs and fb. Each was repeated 10 times. The plot below plot the average of each of the event, and also the standard deviation (the shaded area). The vertical grey bar is the onset timing of the events. From the plot we can see that fb elicits a bigger response than fs does.
plotAverage
plotAverage
You can download the two scripts at:


Receive email notification via email 博客有新内容通知我
文献鸟,永远不错过新文献!

Don't want to miss new papers in your field? Check out Stork we developed:


第二十六期 fNIRS Journal Club 视频

来自上海精神卫生中心的胡志善博士为大家介绍了一篇他们去年发表的综述(静息态近红外在研究发育的应用)。视频如下: Youtube:https://youtu.be/C7xIRrBUhhg Youku: https://v.youku.com/v_show/id_XNTgzNTQ5ODg3Mg==.html
Xu Cui
4 sec read

第二十六期 fNIRS Journal Club 通知 2022/1/15,10:00am

来自上海精神卫生中心的胡志善博士将为大家介绍具体一篇他们去年发表的综述(静息态近红外在研究发育的应用)。热烈欢迎大家参与讨论。 时间: 北京时间2022年1月15日上午10:00地点: https://zoom.com房间号: 897 8179 5073密码: 333858 胡博士要讲解的文章如下: Hu, Liu, Dong, Niu (2020) Applications of Resting-State fNIRS in the Developing Brain: A Review...
Xu Cui
6 sec read

第二十五期 fNIRS Journal Club 视频

来自华东师范大学的胡银莹博士为大家介绍了具体如何计算和验证超扫描实验中脑间同步性,并分享做fNIRS实验相关方面的应用经验。视频如下: Youtube:https://youtu.be/xI_6wKd06io Youku:上传后被youku屏蔽,原因不详。
Xu Cui
3 sec read

5 Replies to “Handy programs to visualize NIRS data (6): plotAverage”

  1. Hi Cui,

    Thanks for your generous contribution, I am just wondering if the normal hyspectral camera can take pictures inside potatos
    Any external light can penetrate the potato body(tub)?

    Thanks lot , if you can provide some confirmation.

    regards,
    Dom

  2. Hi Xu

    We would like to use your scripts to average and plot NIRS data.

    Do you may have sample data to test it? I am especially not sure how the eventOnset (structure, the onset time (in seconds) of event) should look like.

    many thanks in advance
    lisa

  3. @Xu Cui
    Hi Xu, I can’t open the link above. Can you send the example of data again?
    I am in doubt whether the data is the output of NirsLAB block average since the signal event specifies a column vector, but I have been exporting Oxy and Deoxy which results a text document with two columns. Additionally, the time onset differs from participant from another as my finger tapping blocks were randomized, should I create eventOnset for each participant?

    kind regards,
    Artur

Leave a Reply

Your email address will not be published. Required fields are marked *