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. You are always interested in changes relative to another point in time, for example if you investigate a change in oxygenation in response to a stimulus, you are actually investigating the change in response between a short moment before the stimulus was presented and the period in which it was presented. 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.

What is baseline and how to use it?

For those just getting started with using NIRS it can be somewhat unclear what measurements mean. To explain this lets go back to the origin of the baseline.

Most commonly used NIRS is ‘continuous wave’ (CW) NIRS, which is based on the modified Lambert Beer Law. It uses a continuous firing light source. The light will enter the tissue and is both scattered (changing its direction) and possibly absorbed.  Both scattering and absorption are a cause why CW-NIRS provides relative measurements. In the figure below the normal Lambert-Beer Law is shown, wherein absorption in a cuvette is displayed. In the modified Lambert-Beer Law an extra term is added to compensate for scattering in the tissue.

Absorption in a cuvette as described by the Lambert-Beer Law

Absorption in a cuvette as described by the Lambert-Beer Law

The scattering effect is clearly visible when you put your finger in front of a red laser pointer. You will see your whole finger light up, not just a straight line; the light is scattered in the tissue. So, if you would measure directly opposite of the laser on your finger, you would not receive 100% of the emitted light by the laser pointer, even if there was not absorption at all. 
Luckily, we can make the assumption that this scattering in all directions is constant, so if we measure a change in received light, there must a change in absorption in the path that the light followed from the source to the receiver.

Most absorption of NIR-light is by haemoglobin, the very reason why we can utilise NIRS for our measurements. However, the light is also absorbed by other chromophores (e.g. adipose tissue, hair, skin). Again, we make the assumption that this absorption is constant during the measurement and any change in received light is caused by a change in absorption by haemoglobin.

So, CW-NIRS uses a change in received light to calculate a change in concentration of haemoglobin. Therefore the change is always relative to a "starting situation" or baseline.

What does that mean?

CW-NIRS can only measure a change in concentration, therefore it cannot provide you with the starting concentration (so commonly set to an arbitrary zero). However it can provide you with a change from this baseline caused by any kind of intervention (for example contracting a muscle or increased activity in a certain part of the brain). This change is quantified in micromolar (which is micromole haemoglobine per liter of tissue). This can be a negative change, which means a decrease in concentration since the intervention.

How should I use a baseline?

A good baseline can be more difficult than you think. You can use either one time point in your data and set it to zero (by subtracting that value from all data points of that trace), or you can take a baseline for a certain time (e.g. 1 minute) and subtract the average of that from all data points of that trace. If the protocol allows you, it can also be good to record another baseline at the end of your measurement. If the baseline is not significantly different from your initial baseline this gives extra confidence in your data quality, or you might be able to use it for artefact correction.

NEW FEATURE IN SOFTWARE: use period for biasing?

The baseline should be similar to the intervention you want to test, only without that intervention. This seems trivial but experience learns that this can be a challenge. For example during muscle measurements during cycling, a certain resistance is compared to baseline where the subject was sitting still on the bike. This is feasible if you at least make sure that you measure the muscle with the leg in the same position for each subject. However, you might understand that if the position of the leg (pedal down or up) can make a difference for your baseline. It is OK because if you use the same position for all the participants, you have the same ‘starting position’ each time. You do need to be aware of this if you compare with literature. A better solution would be to use cycling at zero Watt for a minute or so and use this as baseline. Now the only difference is the increase in power of the cycling.

Another example for functional NIRS is what you have the subject do when you are recording the baseline. For example when you use certain memory or calculation tasks you must be sure that the subject actually stops his task during the rest/baseline periods. This can be achieved by offering a point to focus on or giving them another task of which you are certain it will not lead to any extra activity in the region that you are focusing on.

How can I use relative concentrations?

Functional NIRS (which part of the brain gets more active whenever a certain stimuli is given) commonly uses multiple channels. Basically, this enables you to see if just a few channels (hopefully the ones over the region of interest) are significantly different than the others. This can then be compared between subject groups.

In some (quite rare) cases researchers just do a resting measurement. They do not use the average values (as these are arbitrary), but they might use the fluctuations in the signal and perform (frequency) analysis. This can be within one signal, or they compare frequencies in multiple channels.

For muscle measurements performing an arterial occlusion might be helpful. Sometimes this is used as a kind of calibration. If the concentration changes reach a certain plateau this is assumed to be a minimal oxygenation state. The maximum shortly after releasing the cuff is assumed to be a maximum oxygenation state. Any changes caused by your actual intervention can be given relative to this minimum and maximum.

Next to this calibration, (venous and/or arterial) occlusions can be used to quantify oxygen consumption, blood volume, blood flow and reoxygenation rates. For more information you are referred to the thesis of Mireille van Beekvelt.

Others do a ‘baseline intervention’ (e.g. a functional task or a sprint) and then do the actual intervention (take a pill, do meditation, follow a certain training) and then do the same intervention as the baseline. Is the change by the second intervention different from the baseline intervention? Do be aware that in this case it would be good to use a placebo as well.

The don’ts of baseline

Do not compare averages of baselines between groups. The average is arbitrary and most commonly set to zero. Do not have too much artefacts (e.g. removing the sensor) between baseline and intervention. Therefore in fNIRS there is commonly a resting period before each stimuli which can be used as baseline.

Lets sum it all up

For easy reference a small list of do's and don'ts for baselines is compiled below:


  • Have a baseline period before your intervention, preferably also after the intervention
  • Be careful with artefacts between the baseline period and the intervention
  • The baseline situation should be as identical as possible to the intervention situation


  • Do not compare the averages of baselines between groups
  • Do not remove the sensor between baseline and intervention

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.



For further information please visit:

Finding Prana:




Image: Finding Prana ISEA 2017 Photo Credit: Juan Waltero

How to create the best optode template for your fNIRS setup

You have probably seen that there are many different templates (or as others also call it, layouts or montages) possible for the OxyMon. How do I choose the one best for me?

How many channels can I create?

First you need to know how many receivers and transmitters your system has. The easiest way is to simply count it in the device itself. The receivers (blue sticker) are on the left of the OxyMon and the transmitters (yellow sticker) on the right. Be aware that two lasers form one transmitter. So, if you count the number of connectors here, divide this by two. This can be seen in Figure 1.

Figure 1: OxyMon cabinet, left: two receivers ("Rx") labelled with a blue sticker and right four transmitters ("Tx") labeled with a yellow sticker

The maximum number of channels that could theoretically be formed with your device is the number of receivers * number of transmitters.

However, this assumes that every receiver is near every transmitter. Especially with systems with a large amount of optodes this is not feasible as some transmitters and receivers will have a distance that is not sufficient to get a signal. For example, a receiver on one side of the head and a transmitter on the other side will not be able to form a channel as the distance is too large to get sufficient light.

Split versus unsplit optical fibers

To make optimal use of your number of receivers and transmitters we offer the possibility to split your optical fiber.

What does this mean?

A simple example using a 2 channel system is shown in the figure below. A 2 channel system has 1 receiver and 2 transmitters. In case you use only unsplit fibers you will get the template as shown at the top. The receiver forms a channel with each transmitter. If you would replace the unsplit fiber for the receiver by a split fiber (see Figure 2), which has 2 ends at the subject end, you will be able to use the template shown on the bottom.


Figure 2:  Two channels using only unsplit fibers (top) versus two channels using an unsplit receiver fiber (bottom)

The advantage of the template on the top is that you now have two channels which can be placed independently on the body. This enables you to have a large amount of channels without the need to buy many receivers. You are required to not place two receiver ends closer than 50mm from each other as this causes crosstalk. The standard multichannel templates available in our Oxysoft software all fulfil this requirement.

The advantage of using an unsplit fiber is that you will have more light. General rule of thumb is that with a full fiber you can increase the interoptode distance with about 5mm in comparison with a split fiber, enabling you to measure deeper in the brain.

By using split fibers it is easier to have a large number of channels of your system. In general, you can never form more channels than ‘receivers’ x ‘transmitters’. If you developed your own template, and you do have more channels, than you have used a (number of) channel(s) multiple times.

Special intermezzo: We also offer a special receiver fiber which is split 8 times! This this fiber can be used to form shallow (or reference or superficial) channels with a short interoptode distance (usually between 5-15mm). Using this fiber, you only need 1 receiver to form up to 8 reference channels!

Choose your template

In the dropdown menu of the optode-template selection screen you will find many different templates you could use. To select the right one for you, you need to know the number of receivers and transmitters you have and the type of fibers (split vs unsplit) you have to your availability. On the bottom right (Figure 3) of the optode-template selection screen you see how many receivers and transmitters are required and which fibers (either 1-end (=unsplit fiber) or 2-end (=split fiber)).

Depending on the template you chose, the software will show you the corresponding NIRS signals for each channel. Do not worry if you chose a template in the software of which afterwards you found that it did not correspond with the actual template that you used on your subject. Oxysoft stores all data from every possible channel. So, it is possible to change the template in the software after finishing a measurement as well.

Tip: If you find a template which uses 1 split fiber, while you only have unsplit fibers, this 1 receiver with 1 split fiber can be replaced by 2 receivers with 2 unsplit fibers.

Tip: If you only have split fibers and the template of your choice has unsplit fibers, it is possible to use just one end of a split fiber by capping off the unused end.

Knowing all this, you can now select the template for your system. If you wish to use another template that can be made with your system or fibers, you can contact us and we can explain what you need to do to use that template.

Figure 3: Template screen from Oxysoft software, an 8 channel split template is chosen, with 2 unsplit receivers (Rx1 & Rx2), 2 unsplit transmitters (Tx1 & Tx2) and 2 split transmitters (Tx3a, Tx3b, Tx4a, Tx4b)

What if the template I want is not in the list?

You can create one yourself! If you go to the folder where Oxysoft is installed (usually C:\Program Files (x86)\Artinis Medical Systems BV\Oxysoft XXX). Here you will find a file named optodetemplate.xml. This file can be edited with any text editor. It includes templates with descriptions which should help you to get on your way. Before you start editing it, do not forget to make a backup. If you need any help, please contact us and we will gladly help you.

How do I choose the best holder for my optodes?

The OxyMon, the fibers and the holders are all separate items therefore a  system can be configured for any application.

As discussed before, the OxyMon can come in many combinations of number of receivers and transmitters, as well as the optical fibers can come split or unsplit. We also offer many options for the holder.For smaller number of channels we usually recommend to use our hard plastic holders. These do not cover large areas of the subjects’ skin and are therefore comfortable and easily accessible.

For larger number of channels (commonly with brain measurements) we advise to use a headcap. We developed these headcaps for optimal use with NIRS. These caps differ in a number of points compared to standard caps. For example they cover a larger area of the prefrontal cortex, have a better optode to skin contact and more coverage of the brain. These caps come with premade holes or without in case you want to determine the exact locations yourself. These caps can be used to in combination with any of the templates predesigned in the software but are also perfect to use when you want to create your own template.

If you need any assistance in determining the right selection for your specific research, please contact Artinis and we are always happy to help you!

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 ( 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 ( 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.


[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.