JOURNAL OF MAGNETIC RESONANCE IMAGING 24:683– 689 (2006)
Original Research
EPI Image Reconstruction With Correction of
Distortion and Signal Losses
Guoxiang Liu, PhD,1,2* and Seiji Ogawa, PhD2
Purpose: To derive and implement a method for correcting
geometric distortions and recovering magnetic resonance
imaging (MRI) signal losses caused by susceptibility-in-
duced magnetic field gradients (SFGs) in regions with large
static field inhomogeneities in echo-planar imaging (EPI).
Materials and Methods: Factors to account for field inho-
mogeneities and SFGs were added in a traditional EPI
equation that was a simple Fourier transform (FT) for ex-
pressing the actual k-space data of an EPI scan. The in-
verse calculation of this “distorted EPI” equation was used
as a kernel to correct geometric distortions and reductions
in intensity during reconstruction. A step-by-step EPI re-
construction method was developed to prevent complicated
phase unwrapping problems. Some EPI images of phantom
and human brains were reconstructed from standard EPI
k-spaces.
Results: All images were reconstructed using the proposed
multistep method. Geometric distortions were corrected
and SFG-induced MRI signal losses were recovered.
Conclusion: Results suggest that applying our method for
reconstructing EPI images to reduce distortions and MRI
signal losses is feasible.
Key Words: EPI; fMRI; distortion; signal loss; susceptibility
effect
J. Magn. Reson. Imaging 2006;24:683– 689.
© 2006 Wiley-Liss, Inc.
IN RECENT YEARS, echo-planar imaging (EPI) has be-
come widely used as a rapid imaging method for appli-
cations such as functional magnetic resonance imaging
(fMRI), diffusion-weighted imaging, and cardiac imag-
ing. In EPI, main field inhomogeneity, large static field
inhomogeneity, and magnetic field gradients or signifi-
cant changes in the susceptibility at tissue/air and
tissue/bone boundaries cause image distortions and
1
Brain Information Group, National Institute of Information and Com-
munications Technology, Kobe, Japan.
2
Ogawa Laboratories for Brain Function Research, Hamano Life Sci-
ence Research Foundation, Tokyo, Japan.
*Address reprint requests to: G.L., Brain Information Group, National
Institute of Information and Communications Technology, 588-2,
Iwaoka, Iwaoka-cho, Nishi-ku, Kobe, Hyougo 651-2492, Japan.
E-mail: lgx@po.nict.go.jp
Received June 22, 2005; Accepted May 18, 2006.
DOI 10.1002/jmri.20672
Published online 4 August 2006 in Wiley InterScience (www.interscience.
wiley.com).
© 2006 Wiley-Liss, Inc.
artifacts (1-4). Susceptibility-related field variation
along the slice-selective direction can result in severe
signal losses, while in-plane inhomogeneity causes geo-
metric distortions. Two distortions usually exist along
the phase-encoding (PE) direction: pixel shift and de-
formation (compression or expansion), which can be
found when a difference exists between the field at a
given pixel and the static field or when a field gradient
exists across individual pixels.
Several methods have been suggested for overcoming
the distortions. Some methods correct the distortion
directly in an image space (5), while others apply a
phase correction to k-space data or use an inverse ap-
proach during image construction (1,6), such as conju-
gate phase reconstruction (CPR) (6), the Weisskoff
method (7), the conjugate gradient method (CGM) (1,6),
and the truncated singular value decomposition (TSVD)
method (1). In addition, single reference scans (8) and a
multireference technique (9,10) have been developed to
reduce the N/2 ghosting and eddy current effect from
fast switching gradients. Also, some authors have re-
ported methods for recovering susceptibility-induced
magnetic field gradient (SFG)-induced signal losses.
The simplest method uses thinner slices to reduce the
field change across a slice (3). However, this method
reduces both the signal-to-noise ratio (SNR) and the
spatial coverage per unit of time. Another method (11–
13) effectively compensates for field inhomogeneities
using multiple refocusing gradients. However, in prac-
tice, many repetitions are needed to sum up to a uni-
form image. This disadvantage limits its value in fMRI
experiments. Some methods using high-order field
compensation (14,15) and a two-shot technique (16,17)
were more efficient but the repetition time (TR) was still
doubled.
Until now, no method has been able to correct distor-
tions and recover SFG-induced MRI signal losses from a
standard EPI k-space, and most previous methods are
not applicable for online processing because of the com-
plicated computation necessary. To overcome the limi-
tations of the previous methods, we have created a new
EPI image reconstruction method that can perform on-
line processing (can be inserted into an MRI reconstruc-
tion system and can reconstruct images in real time)
and recover SFG-induced MRI signal losses.
The standard EPI image reconstruction method (sim-
ple inverse Fourier transformation [FT]) is based on
683
684
assumptions that the field is homogeneous and that
there is no susceptibility difference in the slice. Thus,
the standard EPI equation is just like a simple FT equa-
tion. Of course, with strong field inhomogeneity and
SFGs, an ideal EPI image cannot be reconstructed us-
ing the standard (inverse FT) method. What the MRI
scanner does now is very different from a simple FT.
Our method reconstructs EPI images from a k-space
using the inverse calculation of a “corrected” EPI equa-
tion in which field inhomogeneity factors and SFG fac-
tors are added. Based on this simple idea, we developed
a direct inverse calculation method. Additionally, we
developed a more powerful multistep method that pre-
vents the SFG-induced phase unwrapping problem.
THEORY
In conventional single-shot EPI, the acquired k-space
data, S共m⌬kx, n⌬ky兲, with matrix size N ⫻ N can be
represented as
S共m⌬k x ,n⌬k y 兲 ⫽ 兰兰␳共x,y兲exp共i␥⌬B共x,y兲共nT
⫾ m⌬t兲兲exp共i共m⌬kxx ⫹ n⌬kyy兲兲dxdy, (1)
where ␳共x,y兲 is the spin density of the scanned object, ␥
is the gyromagnetic ratio, n is the nthky line, m is the mth
reading out point, ⫺ Nx/2 ⱕ m ⬍ Nx/2, ⫺Ny/2 ⱕ n
⬍ Ny/2, Nx is the number of data points in the readout
direction and Ny are the phase-encoding steps. ⌬t is the
dwell time, T is the time interval between adjacent ky
lines, ⌬B共x,y兲 is the magnetic field inhomogeneity, and
⌬kx and ⌬ky are gradient area increments in the readout
and phase-encoding directions, respectively. This equa-
tion is used to explain why geometric distortion occurs.
However, the equation does not take into account two
factors: T1/T2 relaxations and intravoxel dephasing by
SFGs. Previous methods (1,5,6,9) based on Eq. [1], cor-
rected geometric distortions well but did nothing to
recover SFG-induced MRI signal losses even though
large SFGs occasionally produced black holes in EPI
images.
SFG-induced MRI signal loss problems have been
studied by many researchers who want to acquire fMRI
data with blood oxygenation level-dependent (BOLD)
contrast using T2*-weighted EPI sequences. Some
methods have reduced these effects (3,4,11–16). Differ-
ent from T1/T2 relaxations, intravoxel dephasing
should not be ignored since it is position-dependent,
like field inhomogeneity. Thus, Eq. [1] should be rewrit-
ten as
S共m⌬k x ,n⌬k y 兲
⫽ 兰兰f sfg 共x,y,m⌬k x ,n⌬k y 兲␳共x,y兲exp共i␥⌬B共x,y兲
⫻ 共nT ⫾ m⌬t兲兲exp共i共m⌬kx ⫹ n⌬kyy兲兲dxdy⬘ (2)
where fsfg共x,y,m⌬kx, n⌬ky兲 is the SFG-induced MRI sig-
nal loss factor, which depends on the intravoxel field
gradient at (x,y) and the time of the relaxation. The
effect of dephasing in MRI signals has been studied
previously. Based on the previous studies (2), we define
Liu and Ogawa
f sfg 共x,y,m⌬k x ,n⌬k y 兲 ⫽ sinc 共koff共x,y兲W/2兲,
where koff共x,y兲 ⫽ ␥G共x,y兲t共m⌬kx,n⌬ky兲
⫽ ␥G共x,y兲共TE ⫹ nT ⫾ m⌬t兲, (3)
where G is the intravoxel field gradient (in the slice-
selective direction), t is the time from excitation to ac-
quisition, and W is the width of the voxel in the SFG
direction (slice-selective direction). The absolute value
of fsfg共x,y,m⌬kx, n⌬ky兲 shows how much the strength of
an MRI signal is reduced by SFG-induced dephasing.
The value of fsfg共x,y,m⌬kx, n⌬ky兲 is bounded on [–1, ⫹1].
When fsfg共x,y,m⌬kx, n⌬ky兲 ⬍ 0, the current voxel ap-
pears in a wrapped phase, which is ␲ bigger/smaller
than in the non-SFG cases, so the SFG factor
fsfg共x,y,m⌬kx, n⌬ky兲 takes into account the signal losses
and the phase wrapping caused by SFG. The SNR will
be increased by this “unwrapped” factor in some strong
SFG cases.
During MRI image reconstruction, an inverse discrete
Fourier transform (DFT) is used instead of an FT. Equa-
tions [1] and [2] can thus be rewritten in discrete form
without any data losses. Equations [2] and [3] can then
be expressed in matrix form as
S ⫽ AI, (4)
where S is the k-space, I is the ideal undistorted image,
and A is the transform matrix operator, which is a
combination of the FT factor exp共i共m⌬kxx ⫹ n⌬kyy兲兲,
the SFG factor fsfg共x,y,m⌬kx, n⌬ky兲, and the field inho-
mogeneity factor exp共i␥⌬B共x,y兲共nT ⫾ m⌬t兲. With a small
SFG and a weak inhomogeneity, the transform matrix
operator A will be close to the FT factor. This is the
assumed condition when the standard FT image recon-
struction method is used. SFGs and field inhomogene-
ity distort EPI images, but fortunately, Eqs. [2]–[4] show
that matrix A can be obtained by measuring the field
and SFG maps and then the ideal image I can be cal-
culated from the k-space using numerical solution
methods, like SVD (1) or CGM (6).
Equations [2]–[4] can be simplified by assuming that
⌬t ⫽ 0. Because ⌬t is much smaller than T, ⌬t
⬍ T/Nx. Equation [4] then becomes
S x ⫽ A x I x , x ⫽ 0,1, . . . ,N x ⫺ 1, (5)
where Sx and Ix are the xth column of S⬘ (the inverse FT
process result of k-space S along the readout direction)
and the ideal image I, and Ax is the Ny ⫻ Ny matrix
defined by
关A x 兴共y k ,y兲 ⫽ f sfg 共x,y,0,y k 兲
⫻exp共i␥⌬B共x,y兲ykT兲
⫻ exp共i2␲yky/Ny兲 y ⫽ 0,1 . . . Ny ⫺ 1
yk ⫽ 0,1 . . . Ny ⫺ 1⬘
(6)
where 共x,y兲 is a pixel of the EPI image, yk is the ykth
readout line. Equation [6] effectively decouples the
NxNx ⫻ NyNy linear system into Nx linear systems of size
NyNy.
EPI Correction of Distortion and Signal Loss 685

Equation 5 can be rewritten to an image equation, field inhomogeneity factors, and is produced by insert-
ing a phase variation into a DFT. ⌰ denotes element-
I x ⫽ A x⫺1 S x , x ⫽ 0,1,. . .,N x ⫺ 1, (7) by-element matrix calculation. When all elements of Asfg
are greater than 0, we define
where Ax⫺1 is the inverse matrix of Ax Since the operator
matrix Ax and a column of the one-dimensional inverse A sfg ⫽ 1 ⫺ A 1⫺sfg . (11)
Fourier transformed distorted k-space Sx are known, in
order to create a column of the EPI image Ix, Ax⫺1 should From Eq. [11], we can obtain
be calculated from Ax. We resolved this problem using
the SVD method (1). Ax is an Ny-dimensional matrix A sfg ⌰A pf ⫽ A pf ⫺ A 1⫺sfg ⌰A pf , (12)
operator that can be expressed in an orthogonal repre-
sentation of the form By and then Eq. [10] can be rewritten as

冘 冘 S ⫽ 共A pf ⫺ A 1⫺sfg ⌰A pf 兲I.
Ny
(13)
Ax ⫽ U VT ⫽ ␴ nu n v nT , (8)
n⫽1
By A⫺1
pf ⫻ Eq. 13, we obtain

where ␴n is the nth singular value and un and vn are A ⫺1 ⫺1

pf S ⫽ A pf 共A pf ⫺ A 1⫺sfg ⌰A pf 兲I
members of the orthonormal sets of vectors in the col-
umns of U and the rows of V. When the system is well ⫽ A ⫺1 ⫺1
pf A pf I ⫺ A pf 共A 1⫺sfg ⌰A pf 兲I.
conditioned, the inverse of the matrix operator Ax is
⫽ I ⫺ A ⫺1
pf 共A 1⫺sfg ⌰A pf 兲I (14)
given as
Then we obtain
冘
Ny
⫺1
1
A ⫽ ជ vជ T .
u (9)
x
␴n n n I ⫽ A ⫺1 ⫺1
pf S ⫹ A pf 共A 1⫺sfg ⌰A pf 兲I. (15)
n⫽1

When field inhomogeneity and SFG factors are too In this equation, we know that A⫺1 pf is the inverse trans-

strong, the system will be ill conditioned, and small formation matrix of FT and field inhomogeneity, so A⫺1 pf S

singular values may be of the same order as the usual is the ideal image when the SFG factor is not taken into
numerical noise encountered in this computation. The account. A⫺1 pf 共 Asfg⌰Apf兲I is the MRI signal loss due to

TSVD method can be used to provide stable solutions in SFG. If we define

order to avoid artifacts from the basis vectors corre-
sponding to those very small singular values. In this I 0 ⫽ A ⫺1
pf S, (16)
method, the singular values are given a threshold and
only those above the threshold are included in the sum- and
mation of Eq. [9]. With appropriate selections of the
truncation level, TSVD can be used as a regularization B ⫽ A ⫺1
pf 共A 1⫺sfg ⌰A pf 兲, (17)
method. However, choosing a truncation level can be
shown to be equivalent to imposing a quadratic con- then Eq. [15] can be rewritten as
straint on the solution.
Unfortunately, such an inverse method does not al-
I ⫽ I 0 ⫹ BI. (18)
ways provide correct results, such as when strong SFGs
make a phase severely wrapped. The problem is that
Then,
the phase is defined only in the principal value range of
关⫺␲,␲兴. Any values outside this range will be wrapped.
During the calculation, the “wrapped phase” problem I ⫽ I 0 ⫹ B共I 0 ⫹ BI兲,
causes errors that lead to incorrect EPI images. The and
problem occurs during the inverse calculation of Ax⫺1

冘
when a calculated phase is wrapped (outside of 关⫺␲,␲兴. N

The basic method of preventing a wrapped phase in-
volves reducing the phase variation in the inverse cal-
culation. This can be done by calculating over multiple
steps. Based on this idea, we rewrote the above equa-
tions. First we separated the transformation matrix A in
Eq. [4] into two matrices,
S ⫽ 共A sfg ⌰A pf 兲I, (10)
I⫽ BiI0 ⫹ BN ⫹ 1I. (19)
i⫽0
The absolute value of all elements of B are smaller than
1, so in Eq. [19], when the number of calculation step N
is big enough, all terms of BN⫹1I will approach 0, so with
an appropriate value for N, an ideal image without dis-
tortion and MRI signal loss can be represented by

冘
where Asfg is the transformation matrix operator for the N

SFG factor, and it can be produced by using Eq. [3]. Apf I⬇ B iI 0. (20)
is the transformation matrix operator for the FT and the i⫽0
686
It is obvious from the equations that to make a recon-
struction kernel, we use A1⫺sfg instead of Asfg. A1⫺sfg can
be calculated using a1⫺sfg ⫽ 1 ⫺ asfg (see Eq. [11]),
where asfg ⬎ ⫽ 0, and asfg and A1⫺sfg are elements of
Asfg and A1⫺sfg respectively. When asfg ⬍ 0, we should
use a1⫺sfg ⫽ ⫺ 1 ⫺ asfg to account for the phase
wrapping caused by SFG.
Equations [16], [17], and [20] are the basic equations
of our reconstruction method. Also, these equations
can be simplified by ignoring the time delay in a readout
line like in Eq. [7], and implementing the inverse calcu-
lation A⫺1pf using TSVD. Different from the direct inverse
calculation method that reconstructs ideal images from
a k-space using one transformation with only one ker-
nel, the multistep method can reconstruct images us-
ing several steps with different kernels. Also these dif-
ferent kernels can be combined into one kernel:
I ⬇ KS
冘
N
K⫽ B i A ⫺1 (21)
pf
i⫽0
where K is the kernel that transforms the k-space S to
the image I.
METHOD
Like many previous methods, two steps are involved in
making an undistorted image. The first step involves
taking a field map scan, calculating the field and SFG
maps, and calculating the kernels based on Eqs. [5] and
[6] by TSVD for the direct inverse calculation method, or
Eqs. [16], [17], and [20] for the multistep method. The
second step involves taking EPI scans and reconstruct-
ing the images using the kernels in a step along the
phase-encoding direction instead of the standard in-
verse fast FT (FFT).
Field Map and SFG Map
Since field inhomogeneity and SFGs produce distor-
tions, the distortions can be corrected by measuring the
field and SFG maps. Before EPI scans, a magnetic field
map must be acquired. The basic principle is to mea-
sure the change in the phase of the MRI signal for two
different echo times. The simplest way to do this is to
acquire two different images with identical parameters
apart from the echo time (TE). A multiecho gradient
echo sequence is used. Previous researchers (18) have
demonstrated that in-plane SFGs (perpendicular to the
slice-selective direction) cause MRI signal losses, too; so
theoretically, to calculate the intra-SFG map, we
should measure a voxel of the EPI in high resolution,
such as the one shown in Fig. 1a. The SFG should not
be calculated along a specific direction. However, the
SFGs in the slice-selective direction are the main cause
of MRI signal losses. In this work, we considered how to
recover these losses. As shown in Fig. 1b, an EPI voxel
is separated only in the slice-selective direction for an
SFG map gradient echo scan. To calculate one pixel in
an SFG map, we used the difference in the phase of the
Liu and Ogawa
Figure 1. Voxel of EPI measured in high resolution for field
and SFG maps. Rz is the slice-selective direction. Rx and Ry
are the readout and phase encoding directions, respectively.
SFG scan MRI signal for two adjacent small voxels in
the slice-selective direction, which are located in an EPI
voxel by:
G ⫽ 共␪ 2 ⫺ ␪ 1 兲/共␥TE sfg D兲, (22)
where G is the local SFG of the EPI voxel in the slice-
selective direction, ␪1 and ␪2 are the phases of two ad-
jacent small SFG scan voxels in the slice-selective di-
rection, TEsfg is the echo time of the SFG scan, and D is
the thickness of the SFG scan (the distance between the
centers of two adjacent small SFG scan voxels in the
slice-selective direction). It can be seen that the SFG
scan is implemented under field inhomogeneity. But
the in-plane field inhomogeneity will not influence the
SFG map calculation, because the two voxels from
which ␪1 and ␪2 are calculated are at the same in-plane
location.
For the direct inverse calculation method, the matrix
Ax is made using the inhomogeneity field and SFG
maps. The kernel matrix of reconstruction along the PE
direction of Ax⫺1 can be calculated using the TSVD
method. Selecting the threshold value is a problem
when the system is ill conditioned. A value of 200 was
used in our experiments. For the multistep method,
A1⫺sfg, Apf, A⫺1 ⫺1
pf , and B ⫽ Apf 共 A1⫺sfg⌰Apf兲 were calculated
from the field and SFG maps.
RESULTS
The reconstruction methods described here were imple-
mented by inserting this algorithm (written in C⫹⫹ on
a SIEMENS IDEA system) into the reconstruction sys-
tem of a 3-T SIEMENS Allegra scanner and applying the
methods to experimental data of phantoms and human
volunteers. The images were acquired using a single-
shot blipped-EPI sequence with centric reordering with
different TE and TR. The field of view was 22 ⫻ 22 cm2,
the matrix size was 64 ⫻ 64, and the slice was 5-mm
thick.
The experimental results of some major correction
methods and our method are shown in Fig. 2. The EPI
images were acquired with a TE of 53 msec, a TR of 113
msec, and a 752-Hz/pixel bandwidth (BW). The PE di-
rection was from top to bottom. There is an air bubble
on top of the phantom seen in Fig. 2a. These figures
EPI Correction of Distortion and Signal Loss 687

Figure 2. Comparison of our method and other methods. a: Gradient echo image; TE ⫽ 10 msec, TR ⫽ 113 msec. b: Original
EPI, TR ⫽ 113 msec, TE ⫽ 53 msec, BW ⫽ 752 Hz. c: Conjugate phase reconstruction. d: Weisskoff method. e: TSVD. f: Direct
inverse calculation method.

illustrate that although the geometrical distortion of an
EPI image can be corrected using the previous meth-
ods, the reduction in intensity by SFGs (mainly around
the air bubble) can be corrected only using our method.
Some MRI images of the brain of a human volunteer
are shown in Figs. 3 and 4. In Fig. 3, EPI distortion was
mainly caused by SFGs and significant changes in sus-
ceptibilities, since the strong field inhomogeneities in
the field map in Fig. 3c could not be found when a
phantom was measured. The susceptibility difference
between tissues and air cavities under this slice lead to
field inhomogeneities, as shown in Fig. 3c, and strong
SFGs, the bright parts in Fig. 3f. Compared with the
gradient echo (GRE) image in Fig. 3a, the one-shot
blipped EPI image in Fig. 3b had geometric distortions
that were caused by the field inhomogeneities shown in
Fig. 3c. The phase-encoding direction of this EPI scan
was from top to bottom, so the weaker field, the dark
area in Fig. 3c, made the eyes appear closer to the top.
Also, in the area close to the air cavity, MRI signals

Figure 3. Experimental results (PE direction from top to bottom). a: Gradient echo image; TE ⫽ 10 msec. b: Original EPI; TR ⫽
500 msec; TE ⫽ 20 msec; BW ⫽ 3002 Hz/pixel. c: Field map. d: Reconstructed EPI image from k-space of (b) using the multistep
method. e: Reconstructed EPI image from k-space of (b) using direct inverse calculation method. f: Intravoxel SFG map.
688 Liu and Ogawa

Figure 4. Other results of the same experiment as in Fig. 3 when our multistep method was used. a: Reconstructed EPI image
when only field inhomogeneity factors were taken into account (the number of calculations of step N ⫽ 1. b: Reconstructed EPI
image when N ⫽ 1. c: Recoveries of signal losses in a pixel (center of the black hole in (a)) in a different calculation step.
d: Projections of 34th (center) column of EPI images (blue: original EPI; green: field inhomogeneities induced geometric
distortions corrected; red: geometric distortions and SFG-induced signal losses corrected). e: Projections of 34th (center) column
of reconstructed EPI images when N ⫽ 1, 2 . . . 20.

appeared with a position shift to the bottom by the
stronger field. Simultaneously, significant signal losses
can be found at the locations of bright areas in the SFG
map in Fig. 3f. The EPI image reconstructed by the
direct inverse calculation method is shown in Fig. 3e. In
this image, the main geometric distortions were cor-
rected, but the signal losses could not be recovered
correctly, and some new severe calculation errors ap-
peared since the inverse calculation system was ill con-
ditioned (too many terms were truncated by TSVD). A
better EPI image is shown in Fig. 3d, which was recon-
structed using the multistep method; both geometric
distortions and signal losses by SFGs were corrected.
Figure 4 shows the advantages of our multistep
method. The image in Fig. 4a can be explained as the
multistep reconstructed EPI image at step zero (when
N ⫽ 0 in Eq. [20]). I is I0 in Eqs. [18]–[20], so MRI signal
losses have not yet been recovered, though the geomet-
ric distortions have been corrected, and the shape of the
reconstructed EPI image is close to that of the GRE
image Fig. 3a. Figure 4b is the EPI image reconstructed
by our multistep method when the number of calcula-
tion step N ⫽ 1. In this image, the signal losses were
recovered incompletely, but when I0 N ⫽ 20 was used,
we got a perfect image shown in Fig. 3d. Figure 4c
shows the recoveries of signal losses in a pixel in differ-
ent calculation step. The correction of geometric distor-
tions and the recovery of signal losses can be illustrated
by Fig. 4d, which shows the difference in projections of
a column in the original EPI image in Fig. 3b, the geo-
metric distortions corrected image in Fig. 4a, and the
final reconstructed image in Fig. 3d. The projections of
a column of reconstructed EPI images when N
⫽ 1, 2 . . . 20 are shown in Fig. 4e. Figure 4c and e
indicate that after step 20, almost no signals were re-
constructed. In other words, nearly all lost signals were
recovered before step 20.
DISCUSSION
The field and SFG map scans can be combined into a
multiecho gradient echo scan, and a slice of the EPI
scan should be separated into several thinner ones to
be measured in the combined field–SFG map scan. The
phases of all small voxels in the field–SFG scan located
in an EPI voxel should be averaged first for calculating
a field map, and the data of all echoes of the combined
field–SFG map scan can be used to construct an SFG
map just like using an SFG map scan.
Our results showed that the EPI image reconstruc-
tion method using a multistep calculation resolved the
SFG-induced phase wrapping problems that caused
bottlenecks in previous approaches. The proposed
methods are based on an inverse calculation of the ideal
EPI equation (considering field inhomogeneity and SFG
factors). Strong SFG factors cause very small singular
values in the inverse calculation and cause the system
to be ill conditioned. This is why the direct inverse
calculation method does not work well with strong
SFGs (Fig. 3e). The multistep method resolves this
problem by separating the SFG factors from the inverse
calculation (Eqs. [17], [19], and [20]). The inverse cal-
culation without the SFG factor works better because
this system can be kept well conditioned Thus, the
multistep method is the main contribution of this work.
EPI Correction of Distortion and Signal Loss
Because it is somewhat sensitive to noise in the field
map, the noise, the SFG map, and their effects on the
reconstruction must be considered. Thus, some prepro-
cessing of the field map and the SFG map (e.g., low-pass
filtering) may be required.
In conclusion, we developed a technique for correct-
ing distortions in EPI images. Different from previous
methods, our method includes the influence of field
inhomogeneities and SFGs, which produce distortion
and MRI signal losses in EPI images, as factors in the
EPI image equation. An inverse EPI image equation that
takes into account these factors is the key part of our
method. In other words, our method is based on not
only the field map, but also the SFG map.
We compared our method with some previously pro-
posed methods. The results showed that our method
corrects both geometrical distortions and moderate
MRI signal losses when SFG maps are measured cor-
rectly.
This EPI image reconstruction approach was com-
bined with an MR system. The system provides practi-
cal, online (real-time) reconstruction. To reconstruct an
image after FFT processing along the readout direction,
we used our algorithm instead of an FFT along the
phase-encoding direction. Thus, the number of compu-
tations rises from n log(n) to n ⫻ n, where n is the size
of the resolution in the PE direction. Our method also
increases the time required to compute our kernel pa-
rameters, but they need to be computed only once for a
given field map and an SFG map. The extra time spent
is worthwhile for correcting a large number of images of
the same slice (in fMRI studies, for instance). In exper-
iments, for a 64 ⫻ 64 –pixel slice, the kernel computa-
tion time was 10 seconds (Windows 2000 operating
system on a 2.8 GHz computer).
We corrected SFG-induced MRI signal loss, which is a
kind of distortion. In future work, we will investigate the
possibility of restoring BOLD signal changes (when
SFG-induced MRI signal losses occur) in fMRI studies.
689
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