Combining the world of NIRS and EEG

Combining the world of NIRS and EEG

EEG and fNIRS are complementary measuring techniques. EEG measures electrophysiological brain activation, that is the electromagnetic field created when neurons in the brain are firing. fNIRS measures the hemodynamic response, that is the change of oxygen in the blood when a brain region becomes active. By combining EEG and fNIRS, a more complete picture of brain activity is obtained: activation of neurons and energy demand of neurons. 

The do's and don'ts of baselines

The do's and don'ts of baselines

A common question we get from our customers is what is a baseline and how to use it. Generally with fNIRS, the absolute values are arbitrary. The period before a stimulus is often referred to as the baseline. In this blog we will describe the do's and don'ts of baselines.

Publication overview 2016

Publication overview 2016

At Artinis we consider ultimate success to be good publications by our customers. To see how we are doing we have systematically searched Google Scholar for NIRS and fNIRS publications.

Finding Prana: An Artist’s Experiment with fNIRS

At Artinis we are regularly surprised with the novel and innovative applications of our fNIRS devices. In this blog we would like to share an example of an unique application by one of our customers.

Helen Collard is an interdisciplinary artist working with yogic pranayama (breathing exercises) and technology. Her most recent project has been working with fNIRS to record the changing levels of oxygenated and deoxygenated hemoglobin whilst performing a sequence of pranayama exercises. In these exercises the breathing is controlled, whilst  the hemodynamic response is sonified in real-time allowing the audience to experience the effects of the pranayama performance on changing hemoglobin levels in an audio form.

Helen has been working in collaboration with by Dr. Philippa Jackson at the Brain Performance and Nutritional Research Center based at Northumbria University, Newcastle, UK. Helen and Philippa used a 2-channel continuous-wave Oxymon system and ran two initial pilot studies to see if the pranayama exercises had significant results to justify creating a sonification system. Once it was established there were clear hemodynamic patterns for each pranayama exercise  Helen began work on making a system to sonify the data in real-time. The system was created by sharing Oxysoft data with programming language Max. The audio is composed to illustrate a sound experience or translation of the body and mind during the pranayama sequence in the audience.

The work is entitled Finding Prana. The title refers to the yoga concept of prana which is a Sanskrit word taken to mean both breath and life and pranayama is the control or regulation of the prana or breath. Finding Prana was most recently performed at the international electronic arts festival ISEA 2017 – the International Symposium of Electronic Arts. Artinis provided a portable Octamon for Helen to make the trip to Colombia and perform at the Manizales Botanical Gardens Auditorium. This year’s symposium and festival attracted an international roster of artists and academics working with technology under the theme of Bio-creation and peace.

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For further information please visit:

Finding Prana: https://helencollardo.com/2016/12/1/fnirs-sonification

ISEA: http://www.isea2017.disenovisual.com/

 

 

Image: Finding Prana ISEA 2017 Photo Credit: Juan Waltero

 
 

3D Digitization and Co-Registration to the MNI brain template using Oxysoft

How do we know that the most active channels are located over the brain region of interest and not somewhere else? Of course, an experienced researcher just knows where to place the optodes, but is that enough to convince a potential highly-critical reviewer or fellow scientist? In order to have stronger evidence for the actual spatial location, one needs a way to measure the position of the optodes reliably. Since 2016, this is possible directly from within Oxysoft using a Polhemus digitizer (http://www.polhemus.com). After measuring anatomical landmarks, simply pointing the digitizer at the optodes is sufficient and Oxysoft reliably knows where the optode is placed with respect to the human head. Oxysoft can visualize this in a 3D view (see Figure 1), allowing not only beautiful picture for a publication, but also having a scientifically sound method to present neuroimaging data. In this article, we will explain how this method works and show how easily it works using Oxysoft.

Figure 1: 3D visualization of activation of a Brite23 measurement in Oxysoft

As every individual head and brain is different, researchers have agreed to use so-called standard brain templates, to which the individual anatomy and functional data is transformed to. Thereby the location of a specific brain region is precisely known, if it is already known from the brain template. The Montreal Neurological Institute (MNI) has created one of these templates, the MNI-152. The International Consortium for Brain Mapping (ICBM) has adopted the MNI-152 brain template as their standard template. This the most used brain template in neuroscience research, especially in the fMRI community. This is also the brain template that is implemented in Oxysoft. Using this template, you are thus using a brain that is compatible with the vast majority of neuroscientists worldwide. For more information on the brain templates, see [1].

Oxysoft supports the digitizers from Polhemus Inc. (see Figure 2). Polhemus is established as the world’s leading digitization and motion tracking company, which devices are not only used extensively in neuroscience research (see e.g. [2] and [3]), but have for example also been used to digitally archive Star Wars artifacts or during filming of the Lord of the Rings movies (http://polhemus.com/scanning-digitizing/case-studies). The Polhemus digitizer measures the position of sensors in a self-created 3D electromagnetic field. Oxysoft uses these 3D coordinates to localize the positon of the optodes with respect to the participant’s head. The tool of choice for digitizing is the stylus. While similar in shape as a pen, it is connected to the Polhemus device. Upon clicking on the button on the stylus, Oxysoft gets notified to record the momentarily position.

Figure 2: Polhemus digitizer on a Brite23. The stylus is used to record the position of the optodes. Head movements are automatically co-recorded using the dedicated head motion sensor.

Oxysoft is the only fNIRS recording software which has this direct interface between fNIRS optode template (also called probe setup) and actual positions of the optodes with respect to the participant’s head. Of course, Oxysoft will automatically coregister the digitized points to the MNI-152 template, allowing you without any effort to report back the actual positions of the optodes in MNI-space.

After having established a connection with the Polhemus digitizer, Oxysoft will initially ask to digitize fiducial points. The fiducials are anatomical landmarks, which are used to infer the size and shape of the participant’s head. Oxysoft will ask for five fiducial points. the nasion (the valley on your nasal bone), the inion (the small bulge on the back of your head), the two pre-auricular points (just in front of your ears) and the vertex, which is the crossing point of the nasion-inion line and the left and right pre-auricular points. Note that using five points allow for a more precise coregistration, and thus more accurate results than used in most articles, and is far superior to the common 4-point registration (see also [2], [3] and [4]). Note that we of course record and correct for movement of the participant simultaneously using a dedicated head motion sensor. The position of these five fiducial points are also known from the MNI template, so that Oxysoft performs the coregistration automatically, i.e. compute the five-point rigid-body transformation.

After some sanity checks whether the digitization was successful, the procedure can seamlessly continue with the digitization of the optodes. As Oxysoft knows the optode template that you are using, it specifically asks for the position of each optode specifically (see Figure 3). Oxysoft then automatically coregisters the optode position and projects it to the scalp surface of the MNI-tempate. You can thus immediately double-check whether the digitization was successful and accurate. In contrast to 3rd party toolboxes, you thus do not need to match the digitized position with the optode, and you overcome the cumbersome search for errors (and sudden enlightment, that you missed an optode and have to start all over again). With this integrated approach, digitization of for example 100-channels takes less than a minute and no additional work from you. You can thus spend more of your valuable time for answering important neuroscientific research questions.

Figure 3: Oxysoft optode digitization screen. Since Oxysoft has a direct interface to the Polhemus digitzer and knows the optode template, Oxysoft directly performs the coregistration of the digitized positions and presents them during the digitization process to you. This way, it is so easy to verify the output of the coregistration and digitization!

Are you interested in obtaining a Polhemus digitizer and the 3D-plugin for Oxysoft? Contact us now! We are happy to provide you with our integrated solution, helping you to get the best out of your research.

References:

[1] Brett, Matthew, Ingrid S. Johnsrude, and Adrian M. Owen. 2002. “The Problem of Functional Localization in the Human Brain.” Nature Reviews Neuroscience 3 (3): 243–49. doi:10.1038/nrn756.

[2] Singh, Archana K., Masako Okamoto, Haruka Dan, Valer Jurcak, and Ippeita Dan. 2005. “Spatial Registration of Multichannel Multi-Subject FNIRS Data to MNI Space without MRI.” NeuroImage 27 (4): 842–51. doi:10.1016/j.neuroimage.2005.05.019.

[3] Whalen, Christopher, Edward L. Maclin, Monica Fabiani, and Gabriele Gratton. 2008. “Validation of a Method for Coregistering Scalp Recording Locations with 3D Structural MR Images.” Human Brain Mapping 29 (11): 1288–1301. doi:10.1002/hbm.20465

[4] Wu, Xue, Adam T. Eggebrecht, Silvina L. Ferradal, Joseph P. Culver, and Hamid Dehghani. 2015. “Evaluation of Rigid Registration Methods for Whole Head Imaging in Diffuse Optical Tomography.” Neurophotonics 2 (3): 035002–035002. doi:10.1117/1.NPh.2.3.035002.

 

 
 

2fNIRS workshop: Hyperscanning with the OctaMon

2fNIRS workshop: Hyperscanning with the OctaMon

Last week Artinis was present at the 2016 2f-NIRS conference in Montpellier, France. This two-day conference, titled NIRS signal: from acquisition to analysis, provided us with a great platform to give a mirror game workshop with two OctaMon devices.