The most common pulse sequences used in fMRI, EPI, and spiral imaging are discussed in detail in Chapter 2. This section will discuss briefly some aspects of these two sequences and alternative strategies that have been investigated to date. If high temporal resolution is desired, most MR imagers are now equipped with the gradient hardware to provide this information with image acquisition times of the order of 40 milliseconds or less. Echo pla- nar imaging and single-shot spiral methods acquire the entire data set for an image from a single excitation pulse, and thus within a single TR. In conven- tional MRI, a separate excitation pulse is used for each line of data acquired, allowing a time, TR, to elapse for the magnetization to recover before the next excitation pulse. Thus, in conventional scanning, an image with 64 phase-encoding steps would require 64 × TR seconds to acquire the entire
dataset. With a TR of 1.5 seconds, this represents an acquisition time of over one minute. Echo planar imaging methods, on the other hand, can collect the data for an entire image in as little as 40 milliseconds. Collecting the data in such a rapid manner does have drawbacks. There is a significant decrease in SNR due to the high bandwidth of the data acquisition, which is needed to collect the data rapidly, and there are also significant distortion effects arising from the accumulation of phase errors over the sampling window.
These distortion effects arise in the phase-encoded direction in EPI, and they are projected in all directions in spiral scanning. This distortion is not present in the conventionally acquired anatomic scans, upon which the activation is usually highlighted. Thus, caution must be used in high-resolution work to ensure that the distorted functional image is registered appropriately to the undistorted anatomic image. This is a difficult problem, as the distortion in the functional images is locally variable; thus, simple rigid body fitting of the two different acquisitions is not sufficient to avoid this problem.45
Methods for reducing the image distortion include moving to multi-shot methods, which of course involves a penalty in temporal resolution. Another approach is to measure in vivo the image distortion, and then use a map of the distortion to correct the final image. Two approaches have been devised to perform this measure; these are field mapping (the image distortion is directly proportional to the distortion in the static magnetic B-field)46–48 and point spread function mapping (PSF).49,50 The field map approach can provide a relatively simple method for correcting image distortions, but it contains no knowledge of the initial distribution of image intensities. This limitation makes it difficult to assign the correct image intensity—and hence functional activation—to the undistorted voxels. The PSF approach can cor- rectly assign the appropriate image intensities to each voxel in addition to correctly locating each voxel in space.
A field map can be obtained using EPI with only two EPI data acquisi- tions. However, because the field map is calculated from the phase difference between these two images, phase wrap can be a problem. This problem can be reduced by collecting several acquisitions with different phase-offsets, thereby making unwrapping of the phase errors much easier. Point spread function maps require a minimum of 16 acquisitions to obtain the PSF in a single direction, but more acquisitions yield higher-resolution PSF maps, and thus better correction of the image distortion. In summary, with acqui- sition times of one minute or less, field maps or PSF maps can be obtained at some point in an fMRI study, allowing correction of the geometric image distortion.
Despite this problem of image distortion, the gain in statistical power in collecting multiple images in a short period of time and the need for acti- vation/control intervals to be short for cognitive reasons necessitates the use of EPI or spiral pulses sequences. Echo planar imaging scans the data space using a raster scan approach and requires state-of-the-art gradients in order to produce high-quality images with minimal image distortion. Spiral scanning, as the name implies, spirals, either in- or out-, from the center of the data space and can be less demanding on the gradient hardware. Most modern magnets now have gradients, which easily ramp as fast as allowed by the United States Food and Drug Administration (US-FDA). The limita- tions currently encountered are not hardware limitations, but are based on subject safety issues. The US-FDA mandates limitations in dB/dt (the rate
at which the gradient can be ramped) because ramping gradients can very rapidly induce current loops in the body that could result in stimulation of muscle groups such as the heart. Small gradient insert coils have been developed that may allow even faster ramping of the gradients, as the active length of the gradients may be short enough to minimize the current loops. These gradient insert systems, however, can be physically restricting, limited in terms of FOV, and are not easily moved in and out of the magnet due to the heavy weight of the combined gradients and cooling system.
Manufacturers have been reluctant to develop such gradient inserts because the coils are awkward to move, weighing several hundred pounds, and they must be properly fastened down each time they are moved lest they torque in the magnet and seriously injure the subject. Going faster also requires faster sampling along the readout gradient, which increases the bandwidth of the data acquisition and negatively impacts the SNR, but with the advan- tage of decreased geometric distortion.
While EPI and spiral gradient echo acquisitions in their many forms are by far the most commonly used approaches, these sequences are sometimes implemented in three-dimensional (3D) acquisition mode,1,9 and besides EPI and spiral scanning, there are many other acquisition strategies that can be adapted to fMRI. Other pulse sequences include asymmetric spin echo imaging51, which combines some gradient echo (T2*) contrast with spin echo (T2) contrast in order to reduce the signal-loss problem associated with static field inhomogeneities and to reduce the contribution of large vessels while maintaining sensitivity to the BOLD affect. Inversion recovery asymmetric spin echo52 has been used to reduce the contribution of CSF to the functional images, reducing the chance of spurious activations arising from pulsatile movement of the CSF.
Fast spin echo imaging15 has been used in MRI, but its sensitivity at 1.5T is too low for most cognitive studies. Variations on the fast spin echo imaging approach include techniques such as GRASE imaging79 and ultra-fast low- angle RARE imaging (UFLARE),80 both of which have similar performance to FSE, but with reduced power deposition that can be particularly important as one moves to higher field strength. These sequences can be applied with or without inversion recovery pulses to reduce the contribution of CSF. FSE, GRASE and UFLARE can all be applied in single-shot mode, but because of the large number of additional rf pulses included in these sequences relative to EPI or spiral imaging, the acquisition window can be long. Longer acqui- sition windows mean fewer slices can be acquired in a TR interval.
A novel technique by Scheffler and colleagues53 uses true fast imaging with steady precession (FISP) imaging and detects signal changes that occur upon activation due to a slight frequency shift associated with local changes in tissue oxygenation. However, this approach requires long TR and a highly uniform static field to be useful.
Single-shot techniques by definition are fast, but there are also meth- ods for accelerating multi-shot techniques. Multi-shot acquisitions are particularly amenable to multi-coil acquisition strategies and the use of sensitivity-encoded (SENSE) reconstruction techniques. In this approach, fewer phase-encoded lines are collected (thereby saving time), but in order to maintain resolution, the FOV is reduced in direct proportion with the number of phase-encoded lines. Reducing the FOV below approximately 20 centimeters when imaging the brain usually results in FOV wrap artifacts
wherein the structures that extend beyond the FOV are folded back over into the image. With multi-coil imaging and SENSE reconstruction, however, the sensitivity profiles of the individual coils making up the multi-coil array are used to unwrap the fold-over artifacts and yield high-quality images in reduced imaging times. Some decrease in SNR occurs, and as the reduction in the number of phase-encoded steps increases, the reconstruction begins to deteriorate, limiting the reductions to factors of two or three. Collecting fewer phase-encoded steps with this approach can be used reduce the imaging time, or it may allow for more slices to be collected within the TR window, thereby increasing spatial coverage without a sacrifice in temporal resolution.
As described above in the discussion on geometric image distortion, increas- ing the acquisition bandwidth also can allow an extra slice or two to be acquired within a given TR because increased bandwidth leads to shorter acquisition windows. However, this shorter readout time will reduce image distortion and SNR; for example, an acquisition with a bandwidth of 64 kilohertz may have a SNR of 50. Doubling the acquisition bandwidth to 128 kilohertz will reduce the image distortion by a factor of two and reduce the SNR by 2and allow a few more slices to be squeezed into the TR interval.