Simultaneous Data Collection of fMRI and fNIRS Measurements Using a Whole-Head Optode Array and Short-Distance Channels

Summary

We present a method for simultaneously collecting fMRI and fNIRS signals from the same subjects with whole-head fNIRS coverage. The protocol has been tested with three young adults and can be adapted for data collection for developmental studies and clinical populations.

Abstract

Functional near-infrared spectroscopy (fNIRS) is a portable neuroimaging methodology, more robust to motion and more cost-effective than functional magnetic resonance imaging (fMRI), which makes it highly suitable for conducting naturalistic studies of brain function and for use with developmental and clinical populations. Both fNIRS and fMRI methodologies detect changes in cerebral blood oxygenation during functional brain activation, and prior studies have shown high spatial and temporal correspondence between the two signals. There is, however, no quantitative comparison of the two signals collected simultaneously from the same subjects with whole-head fNIRS coverage. This comparison is necessary to comprehensively validate area-level activations and functional connectivity against the fMRI gold standard, which in turn has the potential to facilitate comparisons of the two signals across the lifespan. We address this gap by describing a protocol for simultaneous data collection of fMRI and fNIRS signals that: i) provides whole-head fNIRS coverage; ii) includes short-distance measurements for regression of the non-cortical, systemic physiological signal; and iii) implements two different methods for optode-to-scalp co-registration of fNIRS measurements. fMRI and fNIRS data from three subjects are presented, and recommendations for adapting the protocol to test developmental and clinical populations are discussed. The current setup with adults allows scanning sessions for an average of approximately 40 min, which includes both functional and structural scans. The protocol outlines the steps required to adapt the fNIRS equipment for use in the magnetic resonance (MR) environment, provides recommendations for both data recording and optode-to-scalp co-registration, and discusses potential modifications of the protocol to fit the specifics of the available MR-safe fNIRS system. Representative subject-specific responses from a flashing-checkerboard task illustrate the feasibility of the protocol to measure whole-head fNIRS signals in the MR environment. This protocol will be particularly relevant for researchers interested in validating fNIRS signals against fMRI across the lifespan.

Introduction

Cognitive function has been studied in the adult human brain via functional magnetic resonance imaging (fMRI) for nearly three decades. Although fMRI provides high spatial resolution and both functional and structural images, it is often not practical for studies conducted in naturalistic contexts or for use with infants and clinical populations. These constraints substantially limit our understanding of brain function. An alternative to fMRI is the use of portable methodologies that are more cost-effective and robust to motion, such as functional near-infrared spectroscopy (fNIRS)^1,2,3. fNIRS has been used with infants and young children to assess brain function across a range of cognitive domains, such as language development, processing of socially relevant information and object processing ^4,5,6. fNIRS is also a neuroimaging modality especially suitable for testing clinical populations due to its potential for repeated testing and monitoring across ages^7,8,9. Despite its wide applicability, there are no studies quantitatively comparing fMRI and fNIRS signals collected simultaneously from the same subjects with whole-head coverage. This comparison is necessary to comprehensively validate area-level activations and functional connectivity between regions of interest (ROIs) against the fMRI gold standard. Furthermore, establishing this inter-modality correspondence has the potential to enhance the interpretation of fNIRS when it is the only collected signal across both typical and atypical development.

Both fMRI and fNIRS signals detect changes in cerebral blood oxygenation (CBO) during functional brain activation^10,11. fMRI relies on changes in electromagnetic fields and provides a high spatial resolution of CBO changes¹². fNIRS, in contrast, measures absorption levels of near-infrared light using a series of light-emitting and light-detecting optodes². Since fNIRS measures changes in absorption at different wavelengths, it can assess concentration changes in both oxy- and deoxyhemoglobin. Prior studies using simultaneous recordings of fMRI and fNIRS signals with a small number of optodes have shown that the two signals have high spatial and temporal correspondence¹⁰. There are strong correlations between blood-oxygen-level-dependent (BOLD) fMRI and optical measures^11,13, with deoxyhemoglobin showing the highest correlation with the BOLD response, as reported by prior work comparing the temporal dynamics of the fNIRS and fMRI hemodynamic response functions (HRFs)¹⁴. These early studies implemented motor response paradigms (i.e., finger tapping) and used a limited number of optodes covering primary motor and premotor cortex areas. In the last decade, studies have expanded the focus to include a larger battery of cognitive tasks and resting-state sessions, although still using a limited number of optodes covering specific ROIs. These studies have shown that variability in fNIRS/fMRI correlations is dependent on the optode's distance from the scalp and the brain¹⁵. Furthermore, fNIRS can provide resting-state functional connectivity measures comparable to fMRI^16,17.

The current protocol builds on prior work and addresses key limitations by i) providing whole-head fNIRS coverage, ii) including short-distance measurements for regression of non-cortical physiological signals, iii) implementing two different methods for optode-to-scalp co-registration of fNIRS measurements and iv) enabling assessment of the test-retest reliability of the signal across two independent sessions. This protocol for simultaneous data collection of fMRI and fNIRS signals was initially developed for testing young adults. However, one of the goals of the study was to create an experimental setup for collecting simultaneous fMRI/fNIRS signals that can be subsequently adapted for testing developmental populations. Therefore, the current protocol can also be used as a starting point for developing a protocol to test young children. In addition to using whole-head fNIRS coverage, the protocol also aims to incorporate recent advances in the field of fNIRS hardware, such as the inclusion of short-distance channels to measure the systemic physiological signal (i.e., vascular changes arising from noncortical sources, such as blood pressure, respiratory and cardiac signals)^18,19 ;and the use of a 3D structure sensor for optode-to-scalp co-registration²⁰. Although the focus of the present protocol is on the results of a visual flashing checkerboard task, the entire experiment includes two sessions with a mix of traditional block-task designs, resting-state sessions, and naturalistic movie-viewing paradigms.

The protocol describes the steps needed to adapt the fNIRS equipment for use in the MRI environment, including cap design, temporal alignment via trigger synchronization and phantom tests required before the start of data collection. As noted, the focus here is on the results of the flashing checkerboard task, but the overall procedure is not task-specific and can be appropriate for any number of experimental paradigms. The protocol further outlines the steps required during data collection, which include fNIRS cap placement and signal calibration, participant and experimental equipment setup, as well as post-experiment clean up and data storage. The protocol ends by providing an overview of the analytic pipelines specific for preprocessing fNIRS and fMRI data.

Protocol

The research was approved by the Institutional Review Board (IRB) at Yale University. Informed consent was obtained for all subjects. Subjects had to pass MRI screening to ensure their safe participation. They were excluded if they had a history of serious medical or neurological disorder that would likely affect cognitive functioning (i.e., a neurocognitive or depressive disorder, trauma, schizophrenia, or obsessive-compulsive disorder). NOTE: The current protocol uses a CW-NIRS device with 1…

Representative Results

This section presents representative subject-specific responses for the flashing checkerboard task for both fMRI and fNIRS signals. First, representative raw fNIRS data and quality assessments are shown in Figure 6 and Figure 7 to illustrate the feasibility of the experimental setup to measure fNIRS signals in the MRI environment. A diagram of the whole head optode array and sensitivity profile is shown in Figure 8….

Discussion

This protocol for simultaneous data collection of fMRI and fNIRS signals uses a whole-head fNIRS optode array and short-distance channels for measuring and regressing out the systemic non-cortical physiological signals. Critical steps in this protocol include modification and development of the fNIRS equipment for collecting fNIRS signals in the MRI environment. To the best of our knowledge, there is no turn-key commercial system that is fully optimized for capturing simultaneous fMRI and fNIRS measurements usi…

Materials

280 low-profile MRI-compatible grommets for NIRs caps	NIRx	GRM-LOP
4 128-position NIRS caps with 128x unpopulated slits in 10-5 layout	NIRx	CP-128-128S	Sizes: 52, 54, 56, 60
8 bundles of 4x detector fibers with low-profile tip; MRI-, MEG-, and TMS-compatible.	NIRx	DET-FBO- LOW	10 m long
8 bundles of 4x laser source fibers with MRI-compatible low-profile tip	NIRx	SRC-FBO- LAS-LOW	10 m long
Bundle set of 8 short-channel detectors with specialized ring grommets that fit to low-profile grommets	NIRx	DET-SHRT-SET	Splits a single detector into 8 short channels that may be placed anywhere on a single NIRS cap
Magnetom 3T PRISMA	Siemens	N/A	128 channel capacity, 64/32/20 channel head coils, 80 mT/m max gradient amplitude, 200 T/m/s slew rate, full neuro sequences
NIRScout XP Core System Unit	NIRx	NSXP- CHS	Up to 64x Laser-2 (or 32x laser-4) illuminators or 64 LED-2 illuminators; up to 32x detectors; capable of tandem (multi-system) and hyperscanning (multi-subject) measurements; compatible with EEG, tDCS, eye-tracking, and other modalities; modules available for fMRI, TMS, MEG compatibility
NIRStar software	NIRx	N/A	Version 15.3
NIRx parallel port replicator	NIRx	ACC-LPT-REP	The parallel prot replicator  comes with three components: parallel port replicator box, USB power cable and BNC adapter
Physiological pulse unit	Siemens	PPU098	Optical plethysmography allowing the acquisiton of the cardiac rhythm.
Respiratory unit	Siemens	PERU098	Unit intended for the acquisition of the respiratory amplitude (by means of a pneumatic system and a restraint belt).
Structure Sensor Mark II	Occipital	101866 (SN)	3D structure sensor for optode digitization.