Synopsis
We
present an efficient two-sequence protocol for quantifying multiple parameters
in a 1 mm isotropic brain morphometry examination. The protocol comprises a
multiple gradient echo (TE), multiple inversion (TI) time MPRAGE (MEMPxRAGE)
and a two-flip-angle balanced SSFP (TrueFISP) sequence. Proton density and T1 maps
are estimated from the MEMPxRAGE data using the multi-TI data and a Bloch
simulation. With the T1 map and TrueFISP data, the T2 map is estimated using
DESPOT2. Fat, water and B0 maps are obtained from the multi-TE data using the
IDEAL algorithm. The MEMPxRAGE scan
includes embedded 3D EPI-based navigators encoding low resolution functional
information.Introduction
Time
efficiency is paramount in MR examinations, to minimize patient discomfort and
cost, and to minimize the likelihood of motion. We present a two-sequence brain
examination shorter than 10 minutes that yields 1 mm isotropic maps of proton
density (PD), T
1 and T
2 relaxation times, separate water and fat images, and a
B0 field map. The examination also provides a low-SNR T
2* map and a functional
time-series suitable for coarse, low resolution resting state analysis. In
previous work
1 we demonstrated PD and T
1 mapping using a multiple
gradient echo (TE), multiple inversion time (TI) MPRAGE sequence (MEMPxRAGE)
with inner-loop GRAPPA acceleration and volumetric navigators (vNavs) for
real-time motion correction
2. Here we extend this approach by adding
a two-flip-angle balanced SSFP (TrueFISP) sequence, from which T
2 is estimated
3.
With 1 mm isotropic PD, T1 and T2 maps, many contrasts can be synthesized
beyond the original acquisition
4, and images can be resampled in any
plane. We demonstrate that the multiple TE data can be analyzed with the IDEAL
algorithm
5 to extract water and fat volumes
6 and a B0
field map, at 1 mm isotropic resolution. A volume suitable for automatic
cortical and subcortical segmentation by FreeSurfer is generated by combining
the data. The vNavs from the MPRAGE sequence are 3D-EPI-based and T
2*-weighted
(therefore BOLD-weighted)
7.
Methods
The
combined protocol was tested with a volunteer, in accordance with the Partners
HealthCare IRB. The following two scans were collected on a Siemens 3 T Skyra
with a 32 channel head coil: 3D MEMPxRAGE (TR 2530 ms, TE 1.63/3.38/5.13/6.88
ms, TI 1150/2050 ms, flip angle 7°/7°, BW 723 Hz/px, 176 sagittal slices, 256
mm FoV, 1
3 mm
3 resolution, T
acq 5:39 min:s) with embedded
vNavs (TR 20 ms, TE 11 ms, flip angle 2°, BW 4464 Hz/px, 40 sagittal slices,
240 mm FoV, 6
3 mm
3 resolution) and 3D TrueFISP (TR 7.17
ms, TE 3.59 ms, flip angle 15°/70°, geometry and bandwidth match MEMPxRAGE,
T
acq 4:16 min:s).
Results
Figure
1 shows PD and T
1 maps, estimated by fitting the observed MEMPxRAGE data (four TEs,
two TIs) to a table of predictions generated using a Bloch simulation of the
MPRAGE sequence
1,8. From the estimated T
1 data and the two-flip-angle
TrueFISP data, the DESPOT2
3 algorithm was applied to obtain the T
2 map
(also Figure 1). The IDEAL algorithm
5 was applied to the data (four TEs,
first TI) to estimate water and fat signals together with the B0 field map and
T
2* map (Figure 2). FreeSurfer
9,10 was applied to the RMS combined
volume across TEs and TIs. The surfaces and segmentation are shown in Figure 3.
AFNI
11,12 was used to explore the BOLD data in the vNav time series
and extract any apparent resting state networks. Figure 4 shows the frontoparietal control network
13. Figure 5 shows the detected motion
and tSNR.
Discussion
The
MEMPxRAGE accommodates multiple TIs without affecting acquisition time by using
inner-loop GRAPPA acceleration and external reference lines. The multiple TIs
provide information for T
1 estimation, and this informs the T
2 estimate using
the DESPOT2 approach. In previous work we compared the results with DESPOT1
1.
T
2* maps can be estimated as part of the PD/T1 estimation and are also
generated by the IDEAL algorithm. In both cases the T
2* maps are very noisy
because the TEs are very short compared to the expected T
2* values. The incorrect
assumption of a single exponential contributor in each voxel further confounds
the T
2* fit, especially because additional short T
2* components are expected.
Generally, parameter mapping is limited by the model, although the T
1 maps are
relatively stable, and the parameter maps can be used to synthesize arbitrary
contrasts. The simplest combination, the RMS average, provided a combined high-SNR
volume for FreeSurfer segmentation. Although the vNavs are far from optimal for
BOLD imaging (TE and resolution are low), we nevertheless observed fMRI signal
and possibly the frontoparietal control network. tSNR maps indicate a
combination of thermal and physiologic noise. The vNav protocol and supporting
MEMPxRAGE could be modified to further improve BOLD contrast and resolution.
Real-time motion correction is implemented in the MEMPxRAGE sequence and could
be extended to TrueFISP
14. Additional acceleration could shorten the
protocol. This protocol may be useful in clinical populations such as pediatric
patients and Alzheimer’s patients requiring morphometry data in a rapid scan
session. The fat, water and brain segmentation may be useful in MRI-PET scanners
for attenuation correction
15 and partial volume correction of the
PET data
16.
Conclusion
Multiparameter
(PD, T
1, T
2) maps, fat/water separation, B0 mapping, FreeSurfer segmentation and rudimentary functional imaging are
possible with a two-sequence protocol.
Acknowledgements
This
work was supported by NIH NIA R21-AG046657, NICHD R01-HD071664 and R00-HD074649,
NIBIB K01-EB011498 and P41-EB015896, and NIBIB R01-EB019437, the Swiss National
Science Foundation P2ELP2_159891, the Bertarelli Foundation and the Simon’s
Foundation, the Athinoula A. Martinos Center for Biomedical Imaging, and made
possible by NIH NCRR Shared Instrumentation Grant S10-RR023401.References
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