www.elsevier.com/locate/ynimg
NeuroImage 34 (2007) 1506 – 1518
Virtual spatial registration of stand-alone fNIRS data to MNI space
Daisuke Tsuzuki, a,1 Valer Jurcak, a,1 Archana K. Singh, a,c Masako Okamoto, a
Eiju Watanabe, b and Ippeita Dan a,⁎
a
Sensory and Cognitive Food Science Laboratory, National Food Research Institute, 2-1-12 Kannondai, Tsukuba 305-8642, Japan
Jichi Medical University, Japan
c
University of Tsukuba, Japan
b
Received 3 August 2006; revised 24 October 2006; accepted 26 October 2006
Available online 3 January 2007
The registration of functional brain data to common stereotaxic brain
space facilitates data sharing and integration across different subjects,
studies, and even imaging modalities. Thus, we previously described a
method for the probabilistic registration of functional near-infrared
spectroscopy (fNIRS) data onto Montreal Neurological Institute
(MNI) coordinate space that can be used even when magnetic
resonance images of the subjects are not available. This method,
however, requires the careful measurement of scalp landmarks and
fNIRS optode positions using a 3D-digitizer. Here we present a novel
registration method, based on simulations in place of physical
measurements for optode positioning. First, we constructed a holder
deformation algorithm and examined its validity by comparing virtual
and actual deformation of holders on spherical phantoms and real head
surfaces. The discrepancies were negligible. Next, we registered virtual
holders on synthetic heads and brains that represent size and shape
variations among the population. The registered positions were
normalized to MNI space. By repeating this process across synthetic
heads and brains, we statistically estimated the most probable MNI
coordinate values, and clarified errors, which were in the order of
several millimeters across the scalp, associated with this estimation. In
essence, the current method allowed the spatial registration of
completely stand-alone fNIRS data onto MNI space without the use
of supplementary measurements. This method will not only provide a
practical solution to the spatial registration issues in fNIRS studies, but
will also enhance cross-modal communications within the neuroimaging community.
© 2006 Elsevier Inc. All rights reserved.
Keywords: Optical topography; Diffused optical imaging; Transcranial
magnetic stimulation; Probabilistic brain atlas; Talairach coordinate system;
Spatial normalization; Human brain mapping; Clinical application
⁎ Corresponding author. Fax: +81 29 838 8122.
E-mail address: dan@affrc.go.jp (I. Dan).
1
The two authors contributed equally to this work.
Available online on ScienceDirect (www.sciencedirect.com).
1053-8119/$ - see front matter © 2006 Elsevier Inc. All rights reserved.
doi:10.1016/j.neuroimage.2006.10.043
Introduction
Functional near-infrared spectroscopy (fNIRS) is gaining
popularity as a non-invasive tool for monitoring brain activity.
fNIRS utilizes the tight coupling between neural activity and
regional cerebral blood flow and monitors relative regional changes
of hemoglobin concentration (reviewed in Hoshi, 2003; Koizumi
et al., 2003; Obrig and Villringer, 2003; Strangman et al., 2002).
Since fNIRS is a compact experimental system, is less expensive,
easily portable, and relatively tolerant of body movements, it
provides researchers with a means to use a wide variety of flexible
experimental setups for clinical diagnosis and psychological
experiments. fNIRS was only used to monitor a single or a few
channels until the invention of differential illumination technology,
which prevents cross-talk among closely situated illuminators,
enabling up to a few dozen channels to be simultaneously monitored
(Maki et al., 1995). Currently, even whole-head monitoring systems
with more than a hundred channels are commercially available
(Koizumi et al., 2003).
As the number of channels increases, however, it becomes more
tedious to set the optodes. This is one trade off for the convenience of
fNIRS. Ultimately, the region of interest (ROI) tends to be confined
to a smaller number of channels. Along with this, determining
fNIRS channel locations is gaining importance: to realize reproducible fNIRS measurements across subjects and studies, the
channel or optode locations should be statistically defined. Nevertheless, channel locations are only vaguely described in most fNIRS
studies. Considering that an increasing number of studies are being
performed in stand-alone settings, there should be a standardized
way of describing the fNIRS channel locations, preferably in the
common language of neuroimaging.
Meanwhile, there is a strong trend in the neuroimaging
community to represent different brain activation data in a common
anatomical platform, which allows group analysis over multiple
subjects and further comparison across different studies. In pursuit
of a common arena for cross-modal assessment, there appeared a
movement called “probabilistic atlas” for expressing all functional
brain data as entries in a brain atlas that expands into space and time
(Mazziotta et al., 2000, 2001a,b; Toga and Thompson, 2001).
D. Tsuzuki et al. / NeuroImage 34 (2007) 1506–1518
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developed a virtual 10–20 measurement method for already
acquired MR images to extend the reference head–brain database,
and we further developed this method to be applicable to 10–10
and 10–5 systems (Jurcak et al., 2005, 2007). Fourth, we
established a registration method based on the reference head–
brain database, which enables fNIRS data registration on the
standard MNI brain without MRIs of the subject (probabilistic
registration method; Singh et al., 2005). We also described the
error factor associated with probabilistic registration for both
single-subject and group analysis (Singh et al., 2005). However,
careful measurement of 10–20 landmarks and optode positions on
a subject’s head using a 3D-digitizer is necessary to reproduce the
optode placements in the MR images of the reference head–brain
Fig. 1. Alignment of optodes and channels on each 3 × 3 and 3 × 5 holder.
The white and gray circles indicate positions of optodes. When the white
circles are illuminators, the gray circles are detectors, and vice versa. The x's
indicate the positions of channels defined as a midway between neighboring
optode pairs.
Although the term itself is not usually addressed, its concept has
already become widespread as a means of spatial data presentation in
stereotaxic standard coordinate systems such as Talairach or MNI
coordinates (Collins et al., 1994, Talairach and Tournoux, 1988). For
expression of functional imaging data in these stereotaxic systems,
structural brain imaging data are “normalized” or fit to the standard
template brain by linear and nonlinear transformation processes
(reviewed in Brett et al., 2002). The Talairach coordinate system is
based on a single brain specimen with detailed descriptions of
anatomical features including Brodmann estimates (Talairach and
Tournoux, 1988). The MNI system is an extension of the Talairach
system: the standard template of the MNI system was generated by
fitting the brains of multiple subjects to the Talairach template and
subsequently averaging them (Collins et al., 1994). Functional data
are also registered for the normalized brain and hence to the MNI or
Talairach coordinate systems. Accordingly, presenting functional
mapping data on standard coordinate space has become a common
practice for tomographic functional brain mapping methods, such as
functional magnetic resonance imaging (fMRI) and positron
emission tomography (PET).
Despite the increasing importance of standard stereotaxic
coordinate systems in neuroimaging studies, they have only
recently been introduced to fNIRS studies (Okamoto et al.,
2006a,b). Our group has presented a series of papers discussing
the probabilistic estimation of fNIRS channels in standard
stereotaxic coordinate systems. First we created an initial
reference head–brain database presenting a probabilistic correspondence between the 10–20 standard positions in the real world
and the MNI standard coordinate spaces (Okamoto et al., 2004).
Second, we presented an algorithm to automatically project any
given head surface position onto the underlying brain surface
using MRIs of the subject, thereby presenting a theoretical
framework to transform fNIRS data obtained on the head surface
to the cortical surface (Okamoto and Dan, 2005). Third, we
Fig. 2. Various fNIRS optode holders. (A) 3 × 3 rigid holder, top view. (B)
3 × 3 rigid holder placed on a glass head phantom. (C) A rigid holder
cannot fit the head surface perfectly. As indicated by a pencil tip, there is a
gap between the optode holder and the surface of the glass head phantom.
(D) 3 × 5 elastic rubber holder, top view. (E) 3 × 5 elastic rubber holder
placed on a glass head phantom. The holder undergoes elastic global
deformation to fit the head surface. (F) 3 × 5 flexible holder, top view. The
holder is made up of several strips. T-shaped reference strip is highlighted
(black arrow). Examples of flexible strips are also highlighted (gray
arrows). (G) 3 × 5 flexible holder placed on a glass head phantom. The
holder fits the head surface as the angle between neighboring strips
changes slightly (e.g., see skew in the upper left corner indicated by a black
arrow head).
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database. This imposes a certain burden on subjects and thus
limits the application of the probabilistic registration method.
Therefore, in this study, we propose a novel registration method
to realize a 3D-digitizer-free registration of fNIRS data (virtual
registration method). Essentially, the method simulates the
placement of an optode holder on the scalp, taking into
consideration its deformation and the registration of the optodes
and channels onto subjects’ brains. We first describe an algorithm
used to virtually place optode holders onto the head surface.
Second, we examine the validity of the algorithm by comparing the
predicted optode positions and the actual deformations of the
optode holders on spherical phantoms and on real head surfaces.
Third, we demonstrate virtual registration of an fNIRS optode
holder onto MNI space with a simulated group dataset comprised
of 1000 virtual subjects. We include a description of the associated
error factor. Taken together, we present a virtual registration
method for completely stand-alone fNIRS optodes and channels
onto MNI space, based on the guidance of the 10–20 system and
on prior knowledge of optode holder locations and deformations.
Method and theory
Subjects and source MRI datasets
Six healthy adult volunteers (3 males and 3 females, aged 25 to
44 years) participated in the validation study of the deformation
algorithm. Written informed consent was obtained after a complete
explanation of the study. The study was approved by the
institutional ethics committee of the National Food Research
Institute of Japan.
To simulate an fNIRS subject population, we used MRI datasets
acquired from our previous study (Okamoto et al., 2004), which
consist of the whole-head MRI images of 17 healthy volunteers
(Mongoloid; 9 males, 8 females; aged 22 to 51 years). The details of
the methods for image processing and virtual head surface
measurements are described in our previous study (Jurcak et al.,
2005).
General description of fNIRS channel settings
We will begin with a general description of optode holders
and channel setting. We will take 3 × 5 and 3 × 3 holders as
examples. Eight illuminators and seven detectors (or vice versa)
in the 3 × 5 holder, or five illuminators and four detectors (or vice
versa) in the 3 × 3 holder, are alternately placed in a lattice pattern
(Fig. 1). The regions between optodes represent channels where
cortical activation is measured. The actual signal source is
estimated on the cortex as a photon density profile in a space or
plane (Okada and Delpy, 2003; Kawaguchi et al., 2003).
However, reconstruction of the signal sensitivity profile is
beyond the scope of this paper. For simplicity, we will use the
common definition of a channel: the midpoint between optodes
(or its cortical projection point), where maximum photon density
is realized.
Specification of optode holders
Before going into the details of virtual optode placement, it
may be worthwhile to describe current trends in optode holders
because the specifications of a holder influence the exact locations
of optodes.
In the early days, multichannel fNIRS studies used a fixedshape optode holder, where all optodes were placed on a hard
plastic holder molded in a head shape (Figs. 2A, B). Obviously,
there is a technical limitation to using a rigid holder: it does not fit
heads with different sizes well (Fig. 2C). To circumvent this
problem, the optode holder has undergone drastic changes, and
now easy optode placement and better fixation are possible by
using an elastic rubber holder (Figs. 2D, E; Hitachi Medical
Corporation, Kashiwa, Japan) or a flexible holder (Figs. 2F, G;
Shimadzu Corporation, Kyoto, Japan).
Below, we will explain our method of virtual optode placement
using these two types of holders as examples. We will treat them
separately as each type requires a different strategy for reproducible placement and deformation simulation.
Fig. 3. Procedure for reproducible setting of the elastic holder on a head surface. (A) In this example, we select T7 as the reference point on the scalp (green
dot) and place a 3 × 5 holder so that the primary reference optode (the center optode on the lowest row, black dot) aligns with T7. (B) After the alignment, we
rotate the holder around the reference scalp point so that the secondary reference optodes (red dots) are aligned with the reference curve (Fpz–T7–Oz shown in
green) on the scalp in a balanced manner as in panel C. (D) A different strategy uses the secondary reference point (yellow dot), placed on a reference curve
(Fpz–T7–Oz).
D. Tsuzuki et al. / NeuroImage 34 (2007) 1506–1518
Reproducible placement of elastic holder
An elastic holder is usually made by molding the rubber into a
spherical surface so that a universal holder can fit adult subjects
with common head sizes.
In order to achieve reproducible optode orientation, the elastic
probe holder should be placed according to the following guidelines.
First, a given reference optode is set on a reference point on the scalp
(Fig. 3A). Second, two or more secondary reference optodes are
aligned with the reference curve in a balanced manner so that they
are located equidistantly from the reference curve (Figs. 3B, C).
Alternatively, a secondary reference optode is placed on a reference
curve on the scalp (Fig. 3D). If this procedure is followed, elastic
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probe holders can be fixed to scalps across subjects in a reproducible
manner.
Virtual deformation algorithm for elastic holder
When an elastic rubber holder is set on a scalp, it is deformed in
various ways according to the shape of the head. In an attempt to
understand the deformation pattern, we applied the holder to various
surfaces. We found two tendencies. First, deformation occurs in such
a way as to retain the global shape of the holder. Second, the final
fitting adjustment is made by skewing the four corners of the holder.
We developed a deformation algorithm that mimics these tendencies. We generated a virtual optode holder so that optodes are located
Fig. 4. Virtual deformation algorithm for the elastic holder. An example of the 3 × 5 holder is shown. (A) On the head surface, we arbitrarily set a center optode
(black dot) from which we generate a virtual holder. (B) We draw two perpendicular arcs (dotted blue curves) crossing at the center optode. (C) We set secondary
reference optodes (blue dots; primary reference optode shown as a red dot) on the arcs at 30 mm intervals. (D) We set edge points (purple dots) neighboring
secondary reference optodes so that distances from the edge optodes to two neighboring optodes along arcs are 30 mm. (E) We extend the procedure to the four
corner optodes (purple dots). (F) At this point, the virtual holder has deviated from the final destination, so we shift the center optode position (black dot) to yield
a new center optode (black open circle) where we begin a new holder generation as in A. We repeat the above processes until we finally place the holder in the
desired manner as in panel G. The primary reference optode (red dot) is aligned with T7, and the secondary reference optodes (purple arrow heads) are aligned
with the reference curve (Fpz–T7–Oz shown in green) in a balanced manner.
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Fig. 5. Procedure for reproducible setting of a flexible holder on a head surface. (A) In this example, we select T7 as the reference point on the scalp (green dot)
and place a 3 × 5 flexible holder with the reference T-shaped strip (red curves) perpendicularly intersecting at the primary reference optode (black dot). We place
the holder so that the primary reference optode aligns with T7, and the optodes on the reference row (red dots) are well aligned with the reference curve on the
scalp (Fpz–T7–Oz; green curve). (B) We set the holder arbitrarily and adjust its orientation so as to fulfil the rule of setting as in panel C. (D) Another possible
setting is to place the holder so that the secondary reference optode (yellow dot) is on the reference curve (Fpz–T7–Oz) on the scalp.
at equal distances from neighboring optodes and that virtual optodes
are always propagated from the center of the holder.
We will provide a more detailed explanation of how our
algorithm accomplishes virtual holder placement by taking a 3 × 5
optode holder with 30 mm inter-optode distances placed on a given
head surface (Fig. 4). First, we set a temporary point on the head
surface near the expected center of the holder placement (Fig. 4A)
and draw two perpendicular arcs which intersect at that point
(Fig. 4B). Second, we set optode positions for primary and
secondary reference points on the arcs at 30 mm intervals (Fig.
4C). Third, we set edge points so that the distance from an edge point
to two neighboring optodes along the arcs is 30 mm (Fig. 4D).
Fourth, we extend the procedure to the four corner points (Fig. 4E).
However, in order to set the virtual holder to a given target on a scalp,
an additional step was necessary. Virtual holder generation always
starts at the center of the holder, but any optode or channel can be
selected as the primary reference optode or channel (Fig. 4F).
Therefore, we can roughly locate the virtual holder so that the
primary reference optode or channel can be close to the reference
point on a scalp (e.g., T7 in Fig. 4F). Then, we shift the primary
reference optode slightly (Fig. 4F) and re-generate the virtual holder.
If the resulting orientation is not satisfactory, we repeat this
Fig. 6. Virtual deformation algorithm for a flexible holder. An example for a 3 × 5 holder is shown. (A) We set the primary reference optode (black dot) on the
reference point on the scalp, which is T7 in this case (green circle). We draw two perpendicular arcs (red curves) from the scalp reference point, so that the
horizontal arc aligns with the reference curve (Fpz–T7–Oz shown in green) on the scalp. (B) We place secondary reference optodes (blue dots) on the arcs at 30
mm intervals. (C) We set tertiary reference optodes (purple dots) so that distances from two neighboring secondary reference optodes were 30 mm. (D) Similarly,
we set other optodes so that distances from horizontally or perpendicularly neighboring optodes were 30 mm.
D. Tsuzuki et al. / NeuroImage 34 (2007) 1506–1518
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procedure until the location and orientation of the virtual holder
satisfy the given rule of placement (Fig. 4G).
arrange the holder so that the secondary optode or channel can be on
the reference curve on the scalp (Fig. 5D).
Reproducible placement of flexible holder
Virtual deformation algorithm for flexible holder
With a flexible holder, optode holes are connected with short
strips of fixed lengths (Fig. 2F, gray arrows) and a large T-shaped
strip (Fig. 2F, black arrow). The short strips freely rotate, resulting
in three-dimensional deformation, which allows the holder to fit to
a head surface with constant inter-optode distances. Meanwhile,
the T-shaped strip maintains the global shape of the holder by
reducing the freedom of rotations to some extent.
In order to achieve reproducible optode orientation, the probe
holder should be arranged according to the following guidelines.
First, a primary reference optode is set on an optode holder.
Second, a reference row of optodes that crosses the primary
reference optode is set. Third, a column of reference optodes that
crosses the primary reference optode and that keeps a fixed angle
(usually 90°) to the reference row of optodes is set (Figs. 2F, 5A).
To set the holder on a scalp, we need a reference point and a
reference curve that runs through the reference point. First we set
the primary reference optode or channel on the reference point on
the scalp (Fig. 5A). Second, we align the reference column or row
with the reference curve (Figs. 5B, C). Alternatively, we can define
a secondary optode or channel on the reference column or row and
The probe orientation of a flexible holder can be defined using a
relatively simple algorithm. First, a reference optode is set on the
reference point on the head surface (Fig. 6A). Second, the first
reference curve that crosses the reference optode is set on the head
surface, and the optode positions are determined at 30 mm intervals
along the curve (Fig. 6B). Third, we draw a second reference curve
that is perpendicular to the first reference curve and set optode
positions at 30 mm intervals along it (Fig. 6B). Fourth, we set an
additional optode position at 30 mm from the two neighboring
optode positions along the head surface (Fig. 6C), and we repeat
this procedure until all optode positions are determined (Fig. 6D).
Examination of deformation algorithms using spherical phantoms
and real heads
We examined whether the above algorithms allow us to simulate
actual deformation by placing the elastic and flexible holders on
spherical phantoms of various sizes (Fig. 7). To determine the sizes
of phantoms, we examined the curvature of various head regions
using synthetic heads (see Virtual registration for details of synthetic
Fig. 7. Comparison of virtual and actual holder deformation using a spherical phantom. (A) Fixation of a spherical phantom and a transmitter for the 3D-digitizer.
(B) Placement of holder and plotting of the optode position with a color marker. (C) Measurement of the optode positions using the 3D-digitizer. (D) The ideal
sphere in virtual space with a spherical phantom of the same size. (E) An elastic holder (black dots) is generated on the ideal sphere. (F) The actual (black dots)
and virtual (white crosses) optode positions are aligned for comparison.
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heads). We isolated a head surface area that is approximately the
same size as the area covered by a 3 × 3 or 3 × 5 holder. Then we fit a
sphere to the extracted head region using the least square method and
obtained the radius of the best-fit sphere. We randomly selected a
region and orientation from the synthetic heads for 5000 repetitions
to obtain the distribution of the radii of the best-fit spheres. We used
spheres with sizes that cover the 95% confidence interval of the
distribution.
We placed 3 × 3 and 3 × 5 elastic and flexible optode holders on
the spherical phantoms (Fig. 7B). The optode positions were
marked on the spheres, and their positions in the real world
coordinate system were measured with a magnetic 3D-digitizer
(Polhimus) (Fig. 7C). Meanwhile, we generated virtual spheres of
the same sizes as the spherical phantoms (Fig. 7D). On the surfaces
of the virtual spheres, we generated virtual holders (Fig. 7E). We
aligned the actual and virtual optode positions on the surface of the
virtual spheres and compared them (Fig. 7F).
We examined the validity of the algorithms by comparing the
deformations of the holders on actual head surfaces with the virtual
deformations (Fig. 8). In order to make the surface of a subject’s
head as smooth as possible, we covered the head tightly with a
swimming cap and vinyl tape (Fig. 8A). We placed 3 × 5 elastic and
flexible optode holders on the five different regions of the head:
frontopolar, right and left temporal, and the parietal and occipital
regions (Table 3). After marking the optode positions (Fig. 8B), we
measured their positions (Fig. 8C). We included head surface
regions within an additional margin of 15 mm from the regions
covered by the holders and ultimately measured approximately 900
regional head surface positions for reconstruction on the computer
(Figs. 8C, D).
For head surface reconstruction, we smoothed the head surface by
removing protruding points (artifacts during measurement), wrapped
the remaining points with mesh grids, and interpolated the regions
more dense with points at 0.25 mm intervals. Consequently,
approximately 170,000 points comprising a flat surface that matches
a real subject’s head were generated. On the surface of the
reconstructed head surface, we generated virtual holders (Fig. 8E).
We aligned the actual and virtual optode positions on the surface of the
reconstructed head surfaces and compared their positions (Fig. 8F).
Virtual registration
Head shape and size vary among subjects, while the area
covered by an optode holder is relatively invariant. Therefore,
virtual registration of fNIRS optodes and channels onto MNI space
is necessarily accompanied by spatial errors. Error estimation is an
integral issue for virtual registration in order to clearly express the
validity and the limitations of spatial estimations of channel
locations. In our previous study, we described errors associated
with 3D-digitizer-assisted probabilistic registration (Singh et al.,
Fig. 8. Comparison of virtual and actual holder deformation using a real head surface. (A) We smooth the head surface using a swimming cap and fix a transmitter
for a 3D-digitizer. (B) We place an elastic optode holder and plotted the optode positions with a color marker. (C) We measure the locations of optodes and
neighboring head surfaces. (D) The head surface, including optodes (black dots), is realized in virtual space. (E) From the center optode (black dot), we generate
the virtual holder. Virtual optodes are shown in white crosses. (F) A virtual holder (white crosses) thus generated is best aligned to the actual holder positions
(black dots) and subjected to comparison.
D. Tsuzuki et al. / NeuroImage 34 (2007) 1506–1518
2005). We demonstrated a method for a typical group study, and
instead of MR images of subjects, we used our own reference
database comprised of normalized MR images of 17 individuals
(who had not participated in the study). We use a random effects
ANOVA model to elucidate random errors arising from variability
among reference brains and among subjects.
In the current study, we used simulated datasets to assess the
variability among subjects (Fig. 9). Ideally, we would have
preferred real datasets, but we needed a large group for a closer
estimation of the null distribution. Therefore, we simulated our
group data from un-normalized MRI datasets of the 17 individuals
(Fig. 9A) using two parameters: head size (Fig. 9B) and head shape
(Fig. 9C). From the seventeen nasion (Nz) to inion (Iz) observations,
we estimated the distribution of head sizes (i.e., generated the normal
distribution of head size; 185.6 ± 7.5 mm) and randomly assigned a
head size for each simulation according to the normal distribution.
Then, we measured a head shape represented by Nz–Iz, AL–AR (left
and right preauricular points), and m–Cz distances, where m stands
for the gravity center of Nz, Iz, AL, and AR. There is likely to be a
certain degree of coherence between these distances and head size: a
larger Nz–Iz distance would mean larger AL–AR and m–Cz
distances. To preserve this coherence, we used this ratio (Iz–Nz:
AL–AR: m–Cz) to represent the head shape.
We generated synthetic head and brain sets by randomly
combining head sizes and shapes, along with one of the MRI
datasets (Fig. 9D). For each synthetic head and brain, we applied
the virtual holder deformation algorithm to estimate the head
surface points representing fNIRS optodes and channels, projected
the head surface points to the brain (as described in Okamoto and
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Dan, 2005), and obtained the corresponding cortical surface points
(Fig. 9E). In order to register the positional data to MNI space, we
first transformed the data obtained from the synthetic head and
brain back to the original MRI dataset. We then transformed the
positional data to MNI space using our in-house program, as
previously described (Okamoto and Dan, 2005). We repeated the
above procedure 1000 times. The common estimate and estimation
error for each optode or channel location are calculated in MNI
space as mean and standard deviation for the 1000 simulated
datasets (Fig. 9F).
Results
Examination of deformation algorithms using spherical phantoms
We examined whether holder deformation algorithms can simulate
actual deformation by placing elastic and flexible holders on spherical
phantoms. Prior to the physical measurements, we used virtual heads
to explore the range of spheres that fit the curvature of various head
regions. Fig. 10 shows the distribution of the radii of the best-fit
spheres. For 3 × 5 holders, the minimum and maximum radii were 60.2
and 183.6 mm, respectively; the 95% confidence interval was 68.6 to
127.1 mm. For 3 × 3 holders, the minimum and maximum radii were
55.6 and 245.9 mm, respectively; the 95% confidence interval was
64.2 to 136.9 mm. Accordingly, we used spheres with radii of 62.5 to
223 mm to investigate deformation algorithms.
For 3 × 5 elastic holders, we set the primary reference point for
holder placement at the center, and its horizontally neighboring
point as the secondary reference point. For 3 × 5 flexible holders,
Fig. 9. Flow chart for the virtual registration method. First, we randomly choose one of the MRI datasets (A) and combine two parameters: a head size parameter
(Nz–Iz distance) from the normalized head size distribution (B), and a head–shape ratio (Nz–Iz, AL–AR, and m–Cz ratio) (C), to generate a synthetic head and
brain set (D). We then apply virtual holder deformation to estimate optode and channel locations on head (blue dots) and brain (red dots) surfaces (E) and transfer
the spatial information to the MNI space. We repeat this procedure (A–E) 1000 times. From the 1000 datasets, we calculate common estimates and estimation
errors for each optode or channel location in MNI space (F).
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were negligible (less than 2 mm) for all the cases examined.
Therefore, we concluded that the algorithm can closely mimic the
deformation of elastic and flexible holders.
Demonstration of the virtual registration method
Now that the virtual holder deformation algorithms have been
validated, we will demonstrate how to implement the virtual
registration method in actual situations. We prepared the placement
of the holder on five different scalp regions, as summarized in
Table 3. We used elastic and flexible holders for this demonstration, but it should be noted that we used slightly different rules for
placing the holders to enhance their deformation characteristics,
but not to evaluate which is better. The results of virtual
registration for optode positions on the scalp and their cortical
projections are shown in Fig. 11. In all cases, the centers of the
circles represent the most likely estimate and their radii represent
the standard deviation of displacement in MNI space. In terms of
lower error rates, spatial estimates were most stable in the
frontopolar region, followed by temporal regions, and the parietal
region, and were the least stable in the occipital region. This
regional tendency is the same as the correlation of 10–20 positions
and MNI space as we used them as guidance for optode holder
placement. However, estimation errors remain within 13 mm. This
is a reasonable compromise for virtual registration without MR
images and digitizer measurements.
Discussion
Fig. 10. Distribution of the regional curvatures for the scalp regions covered
by (A) 3 × 5 holders and (B) 3 × 3 holders. The distributions are based on
random placement simulations of the virtual holders for 5000 repetitions.
we set the center point as the primary reference point, and the
reference curves to cross perpendicularly at the center of the
holder. We also tested the deformations of 3 × 3 elastic and flexible
holders. The results are summarized in Table 1.
The discrepancy between the simulation using the virtual holder
deformation algorithm and the actual holder deformation was
negligible (less than 2 mm) for most cases. The only exception was
fitting a 3 × 5 elastic holder on a 125 mm sphere, where the
maximum deviation was 2.9 mm. However, as demonstrated in the
regional best-fit sphere simulation, such an extreme case is
unlikely in actual situations. Therefore, we concluded that the
algorithm for the virtual holder registration is valid for spheres that
correspond to most adult scalp surfaces.
Examination of deformation algorithms using real heads
Although spherical phantoms can be used to accurately simulate
extreme deformations in optode holders that may occur with both
small and large heads, rather complex deformations occurring on
actual head surfaces with irregular shapes may be beyond their
scope. Hence, we examined whether the above algorithms can be
used to simulate actual deformations on a head surface by placing
the holders onto four different regions of the head surfaces of six
subjects. The results are summarized in Table 2.
Discrepancies between simulations using the virtual holder
deformation algorithm and actual holder deformation on real heads
As presented above, our method makes the virtual spatial
registration of stand-alone fNIRS optodes and channels onto the
MNI space possible. Here we would like to discuss how this
method can facilitate fNIRS research, especially in a more global
context surrounding the whole neuroimaging community.
Neuroimaging techniques serve not only neuroimaging research,
but also as important tools for other scientific disciplines. In this
perspective, fNIRS has great potential. Its affordability, compactness, and less restrictiveness allow flexible experimental settings
and thus can contribute to the expansion of the frontiers of functional
neuroimaging research. For this purpose, data sharing within the
neuroimaging community is essential. By describing fNIRS data on
common stereotactic coordinate systems, cross-reference between
fNIRS data and functional and anatomical data obtained by other
neuroimaging modalities is made possible. The current study
presents a practical and fair solution to this data sharing issue.
Table 1
Examination of deformation algorithms using spherical phantoms
Diameter
(mm)
125
148
197
248
296
446
Elastic
holder 3 × 5
Flexible
holder 3 × 5
Elastic
holder 3 × 3
Flexible
holder 3 × 3
Max
Avg
Max
Avg
Max
Avg
Max
Avg
2.9
1.2
1.0
0.6
0.7
1.3
1.1
0.6
0.5
0.3
0.3
0.6
1.3
1.5
1.2
0.8
0.9
0.6
0.7
0.7
0.6
0.3
0.4
0.3
1.7
0.8
1.0
0.5
0.4
0.8
0.7
0.4
0.5
0.3
0.3
0.4
0.8
0.7
1.4
1.0
0.7
0.5
0.5
0.3
0.6
0.3
0.4
0.3
Max represents the maximum deviation between actually and virtually
deformed holders. Avg represents the average deviation for all the optode
positions on the holder tested. Both Max and Avg are presented in mm.
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D. Tsuzuki et al. / NeuroImage 34 (2007) 1506–1518
Table 2
Examination of deformation algorithms using real heads
Head region
Subject 1
Subject 2
Subject 3
Subject 4
Subject 5
Subject 6
Max
Avg
Max
Avg
Max
Avg
Max
Avg
Max
Avg
Max
Avg
1.4
1.5
1.4
1.0
0.7
0.8
0.6
0.6
1.6
1.7
1.8
1.0
0.7
0.8
0.7
0.5
1.8
1.6
1.3
1.2
0.7
0.7
0.6
0.7
1.3
1.0
1.8
1.5
0.8
0.7
0.7
0.6
1.2
1.3
1.6
1.6
0.5
0.7
0.8
0.6
1.5
1.1
1.3
1.0
0.6
0.5
0.8
0.5
Flexible holder (3 × 5)
Frontopolar
1.4
Occipital
1.9
Left temporal
1.8
Right temporal
1.4
0.6
0.9
0.9
0.8
1.9
1.2
1.5
1.7
0.9
0.6
0.7
0.6
1.5
0.9
1.2
1.2
0.8
0.6
0.6
0.6
1.6
1.4
1.2
1.7
0.8
0.9
0.6
0.8
1.3
1.1
1.6
1.3
0.7
0.7
1.0
0.6
1.4
1.6
1.4
1.3
0.7
0.8
0.8
0.7
Elastic holder (3 × 5)
Frontopolar
Occipital
Left temporal
Right temporal
Max represents the maximum deviation between actually and virtually deformed holders. Avg represents the average deviation for all the optode positions on the
holder tested for each participant. Both Max and Avg are presented in mm.
In previous studies, we described a 3D-digitizer-mediated
method that enabled probabilistic registration of fNIRS optodes
and channels onto the MNI standard coordinate system (probabilistic registration method; Singh et al., 2005). However, the
probabilistic registration method requires some additional measuring time, and this may not be desirable, especially in emerging
clinical situations such as pre-surgery language dominance
determination (Watanabe et al., 1998), preoperative planning for
tumor removal (Fujiwara et al., 2004), focus diagnosis of epilepsy
(Watanabe et al., 2000, 2002), rehabilitation monitoring (Miyai
et al., 2001, 2003), psychiatric diagnosis (Ehlis et al., 2005;
Fallgatter and Strik, 1997, 1998, Suto et al., 2004; Kameyama
et al., 2006), and postoperative cerebral oxygenation monitoring
(Murata et al., 2003; Hoshino et al., 2006). The virtual
registration method demonstrated in the current study provides
a promising alternative solution to spatial registration issues in
fNIRS studies, especially for clinical applications.
The virtual registration method has two prerequisites. First,
probe holders for fNIRS are set in a reproducible manner,
preferably with the guidance of a stable scalp landmark setting
such as the international 10–20 systems or its derivatives, or the
10–10 or 10–5 systems (Jasper, 1958; Chatrian et al., 1985; Nuwer
et al., 1998; Klem et al., 1999; Oostenveld and Praamstra, 2001).
Second, the deformation of a probe holder should, to a certain
degree, follow predictable patterns. As long as these prerequisites
are satisfied, the virtual registration method presented in the current
study enables fNIRS optode and channel positions to be registered
on standard stereotaxic brain coordinate systems, including the
MNI system, without using any additional devices. In this study,
we used two probe holders for demonstration only because they
were locally available. Since virtual registration algorithms can be
developed for any probe holders that deform in predictable ways,
we are planning to extend virtual registration algorithms to other
types of probe holders.
The accuracy of the estimations of the virtual registration
method is approximately the same as that of the 3D-digitizermediated probabilistic registration method (Singh et al., 2005). For
most of the lateral cortical regions, the errors of estimation,
expressed as standard deviations, are approximately 1 cm. This
range of spatial error may be sufficient for most functional studies,
provided that the widths of major gyri are approximately 1 cm.
However, spatial errors were not identically distributed among
brain regions, e.g., we observed larger errors in the virtual
registration in the occipital region. This is primarily because virtual
registration is affected by errors of nearby reference positions (i.e.,
10–20 positions) used for transformation to MNI standard
coordinate system (Okamoto et al., 2004; Singh et al., 2005;
Jurcak et al., 2007). In the occipital region, reference positions are
relatively large mainly due to unambiguity in inion location
thereby causing larger errors. Such large errors cannot be avoided
as long as we use 10–20, 10–10, or 10–5 systems for placing probe
holders. In search of improved virtual registration, we are looking
for plausible alternative to conventional 10–20, 10–10, or 10–5
systems.
One major obstacle of the current study is how users can apply
this method in practical situations. The procedures used in the
current study are not very straightforward, requiring the user to
provide many parameters and small adjustments for each virtual
holder registration. We are planning to modify the program to store
the results of virtual holder registrations as an empirical database,
so that the users need not spend time inputting the same
parameters more than once. Since many previously published
Table 3
Specifications for holder placement used to demonstrate virtual registration method
Scalp region
Reference optode
Reference row
Reference point on the scalp
Reference curve
Frontopolar
Occipital
Left temporal
Right temporal
Parietal
[3,3]
3
Fpz
T7–Fpz–T8
[3,3]
3
Oz
T7–Oz–T8
[3,3]
3
T7
Fpz–T7–Oz
[3,3]
3
T8
Fpz–T8–Oz
[3,3]
3
Cpz
T7–Cpz–T8
For example, the frontopolar column is read as the reference optode on the third row of the third column of the holder, which is placed on Fpz so that the third
optode row aligns to the T7–Fpz–T8 reference curve.
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D. Tsuzuki et al. / NeuroImage 34 (2007) 1506–1518
Fig. 11. Demonstration of virtual registrations. Cases for elastic holders are shown. Virtual holders were placed on five different regions on the head: (A)
frontopolar, (B) occipital, (C) left and (D) right temporal, and (E) parietal regions. They were projected onto the cortical surface (F–J). Rules for placement are
summarized in Table 3. Red circles indicate the optode positions for elastic holders. Centers of circles represent the most likely estimates and their radii represent
the standard deviation of displacement. Axes are correspondent to those in MNI space.
D. Tsuzuki et al. / NeuroImage 34 (2007) 1506–1518
fNIRS studies satisfy the prerequisites mentioned above, we are
planning to re-examine them spatially.
It is important to note that the virtual registration method is
sensitive to the type of holder used, and how it is set. For example,
what seems to be a detailed description (e.g., “we placed the center
of the lower optode rows of 3 × 5 optode holders with an interoptode distance of 30 mm at Fpz, and the remaining four lower
optodes were aligned with the Fp1–Fpz–Fp2 line”) is not sufficient
to correctly place a virtual holder. The type of holder used must
also be included. There is another important pitfall. We have to
make sure that the inter-optode distance remains exactly the same.
For example, a commercial, flexible holder uses a patch between
holder and head to ensure a comfortable fit, but, depending on the
head size, this patch results in a change in inter-optode distance.
We have already incorporated this parameter into our simulation. In
general, any careful reports on the methods used are preferred.
Although the current method is optimized for fNIRS studies, it
could be easily modified for transcranial magnetic stimulation
(TMS) mapping data (Wassermann et al., 1992; Brasil-Neto et al.,
1992), which are typically represented by regional mesh grids
developed on a scalp and are topographically similar to an fNIRS
optode holder. However, the current algorithm is optimized to
simulate probe positioning based on two commercially available
fNIRS optode holders and needs further modification to be applied
for TMS studies.
In conclusion, this study serves as an important practical
extension to our series of studies. The virtual registration
method enables the registration of multi-subject or single-subject
fNIRS data into the MNI coordinate system not only without
structural MRIs of the subjects, but also without a 3D-digitizer.
Reporting fNIRS data in MNI space is only recently becoming a
common practice. However, with the methods presented in this
study, this practice will become readily accessible. The use of
common stereotaxic platforms will make it possible for fNIRS
researchers to have access to a wealth of neuroimaging data
expressed in MNI and Talairach spaces and also to convenient
tools available in these spaces, such as a maximum probability
atlas (Hammers et al., 2003) and computer-assisted anatomical
labeling (Lancaster et al., 2000; Le Goualher et al., 1999;
Nowinski and Belov, 2003; Tzourio-Mazoyer et al., 2002). On
the other hand, the presentation of fNIRS data in common
stereotactic space will help all neuroimaging researchers understand and assess fNIRS data. Thus, we believe that the current
study will enhance multi-modal communication within the
neuroimaging community.
Conflict of interest statement
All authors hereby declare that they have no financial and
personal relationships with other people or organization that could
inappropriately influence our work.
Acknowledgments
We thank the subjects who participated in this study. We are
grateful to Dr. Haruka Dan for her helpful advice. We thank
Ms Akiko Oishi for preparation of the manuscript and data,
and Ms Melissa Nuytten for examination of the manuscript. This
work is partly supported by the Industrial Technology Research
Grant Program in 03A47022 from the New Energy and Industrial
Technology Development Organization (NEDO) of Japan, and
1517
Grant-in-Aid for Scientific Research 18390404 from the Japan
Society for the Promotion of Science.
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