MR protocols for imaging at UCSF are categorized by anatomic location and by indication, so that disease-relevant abnormalities can be consistently identified and characterized. Although vendor- and techniquerelated variability is to some degree unavoidable across different scanners, this approach to protocol development helps to standardize acquisition techniques for consistent image quality across the multiple MR systems used for pediatric patients in our practice and to facilitate longitudinal follow-up when monitoring changes in disease over time. Each protocol specifies the field of view (FOV), matrix size, and slice thickness for the desired spatial resolution and anatomic coverage. The protocol also specifies appropriate scanning parameters, including flip angle (flip), repetition time (TR), echo time (TE), number of signal averages (NEX), readout bandwidth (BW), and, if appropriate, the echo train length (ETL) and inversion time (TI). These technical parameters may differ slightly for different scanner vendors and field strengths. Finally, specifics regarding fat and flow suppression and which reformats should be routinely generated are also included in protocols. The fundamental elements of these protocols are outlined below by body part, in a similar fashion to how they are organized in our practice.
The primary pulse sequences used for the evaluation of brain structure are summarized in Table 1-1
. T1- and T2-weighted images are obtained using gradient-recalled echo (GRE) and fast spin-echo (FSE) techniques. Although it sometimes provides the best contrast, singleecho spin-echo acquisition requires longer scan times and is now less commonly used. Given its short imaging time and sensitivity to a broad range of diseases, diffusion-weighted imaging (DWI) is included in almost all brain protocols. Although state-of-the-art DWI is also capable of depicting brain anatomy in high detail, we defer discussion of this technique until the next section, which focuses on physiologic and metabolic MR techniques. In our practice at UCSF, susceptibilitysensitive (T2*-weighted) imaging is also included for most indications.
High-quality T1-weighted imaging is essential for accurate identification of structural brain abnormalities. Volumetric 3D T1 GRE techniques such as spoiled gradient echo (SPGR) and magnetizationprepared rapid gradient echo (MP-RAGE) (52
) are favored as, unlike conventional 2D FSE, the resulting images can be reformatted in any
plane, exhibit strong contrast between gray and white matter, and allow high spatial resolution to be achieved within clinically feasible scan times using short TR and TE (typically 35 ms for TR and minimum TE). Using a sagittal prescription oriented such that the longest (craniocaudal) axis is the readout direction, the total acquisition time for this sequence is approximately 5 minutes for 3 T scanners. The FOV and matrix size for 3D T1 imaging in children should be set so that the voxel size is no greater than 1 × 1 × 1 mm.
When contrast-enhanced T1-weighted imaging is necessary, we use slightly different parameters with 3D T1 GRE sequences in order to heighten sensitivity to the T1-shortening effects of gadolinium. If volumetric images cannot be acquired, T1 fluid-attenuated inversion recovery (FLAIR) or FSE sequences can be used instead. Although T1 FLAIR gives better T1 information than do FSE sequences, a T1 FSE with TR/TE = 600/minimum sequence can be routinely used for T1-weighted images on 1.5 T scanners.
Although 3D T1 GRE acquisition is useful for identifying small lesions given its superior spatial resolution, T1 FSE is the sequence of choice when paramagnetic contrast is to be administered. Use of this imaging sequence produces excellent images with greater enhancement contrast; moreover, the imaging time is shorter than with most inversion recovery sequences, resulting in less motion artifact. Spin-echo T1 images do not work as well at 3 T due to the prolongation of T1 relaxation times, however. Therefore, T1 FLAIR (usually using short TE in the range of 20 ms and TI = 750 ms) sequences are used; these give excellent T1 weighting but do not depict contrast enhancement as well as do FSE or 3D T1 GRE images.
Anatomic detail can be visualized well using 3D T1 by reformatting the acquired images to the optimal planes that depict different structures. For example, we find that sagittal images are best for evaluating the corpus callosum, pituitary gland, hypothalamus, and cerebellar vermis, common locations of pediatric brain tumors. They are also excellent for assessing the lateral convexities of the cerebral hemispheres, especially around the sylvian fissures. Ventricular morphology, the septum pellucidum and brain stem are seen well on axial images, and the cerebellar hemispheres, temporal lobes, skull base, and commissural white matter tracts are well evaluated on coronal images. 3D technique is very valuable in the imaging of tumors, where the relationship of the mass to the surrounding brain and dura is of great importance to the neurosurgeon. As 3D T1 acquisition techniques are increasingly standardized across vendors, this sequence is also gaining importance for its role in computational structural analysis, automated diagnosis, and statistical comparisons with atlas-based reference data (53
For T2-weighted imaging, the ETL for FSE acquisition should be kept low (≤4) in order to achieve satisfactory contrast without sacrificing spatial resolution. With parallel imaging, it is now possible to obtain volumetric T2-weighted images using variable flip angle FSE techniques (CUBE, SPACE, VISTA). Although these enjoy high spatial resolution, we have found that the tissue contrast that results with these methods is not yet sufficient to use for routine imaging protocols in children. Instead, we most often employ traditional multislice (2D) FSE acquisition with 4- to 5-mm slices (2-2.5-mm gap). Dual short and long echo FSE is used, with TR/TE = 3000/60, 120 ms in infants less than 12 months old and TR/TE = 2500/30, 80 ms otherwise. More heavily T2-weighted sequences are recommended in the first year of age, as the water content of the brain in young children is considerably higher than in older children and adults (55
). In this patient group, we use TR/TE = 3000/120 ms. Others have used a dual-echo short tau inversion recovery (STIR) sequence with TR/TE/TI = 5400/128/130 ms (23
), although in our experience noise in STIR images can sometimes make them difficult to interpret. Variable flip angle 3D FSE, although it does not enjoy the same level of tissue contrast, can be useful to supplement 2D FSE in patients with epilepsy to identify sulcal and gyral morphological abnormalities.
Some authors have advocated the use of T2 FLAIR to look for regions of abnormal T2 prolongation. In our experience and that of others (57
), FLAIR images are not sensitive to cerebral pathology in neonates or infants, but are useful in older children in whom myelination is complete or nearly complete. We do not use FLAIR as a primary sequence in infants, but we do sometimes use it as a secondary sequence for lesion characterization. In children beyond the age of 2 years, when myelination is nearly complete, FLAIR becomes a part of our routine protocol because of its high sensitivity for subtle supratentorial lesions, particularly in the cerebral cortex and periventricular white matter. Sargent and Poskitt found that FLAIR is complementary to T2-weighted infants in children (58
). They found FSE T2 FLAIR to have better CSF nulling and better gray matter-white matter differentiation than echo-planar FLAIR.
3D T2 FLAIR using CUBE, SPACE, or VISTA (depending on the scanner manufacturer) is our preferred method for T2 FLAIR acquisition. These have the benefit of very high spatial resolution of 1 to 2 mm and relatively short imaging times of 5 to 6 minutes and like volumetric gradient echo T1 images can be reformatted in any plane. Similar to all 3D techniques, longer imaging times render 3D T2 FLAIR sequences more susceptible to artifacts from patient motion, and in our experience, the tissue contrast of such sequences does not always compare favorably to 2D sequences.
It should be emphasized that in patients less than 18 months of age, both T1- and T2-weighted images are necessary for accurate interpretation. Brain maturation is evaluated best by T1-weighted images from birth to 6 months of age. However, from 6 to 8 months of age until approximately 24 months of age (at which time the brain is essentially mature by MR standards), T2-weighted images are more useful for assessing myelination and brain maturity (see Chapter 2
for more details on timing of brain maturation). During the process of white matter maturation, the cerebral cortex and subcortical white matter of the brain become isointense for a variable period of time on MR images; this loss of intrinsic contrast obscures structural detail. Therefore, during the first 8 months of life (while the white matter is maturing on T1-weighted images), T2-weighted images are required to see the details of the gyral and sulcal patterns. Similarly, as white matter matures on T2-weighted images between 8 and 24 months of age, T1-weighted images are essential for evaluation of structural abnormalities.
A significant drawback of T2-weighted and FLAIR sequences is longer imaging times when compared to T1-weighted imaging. Some extremely fast MR techniques can be used in selected cases without sedation. These include the previously discussed ssFSE (59
) and PROPELLER (61
); both are most useful for gross assessments such as ventricular size in patients with hydrocephalus or follow-up of extraparenchymal fluid collections. PROPELLER has the advantage of better contrast to noise, more flexible contrast, and the ability to compensate for motion by retrospectively correcting the acquisitions (called “blades”), but has the disadvantage of slightly longer acquisition times (61
). When we do use PROPELLER FSE, the parameters applied as TR/TE = 4000/83 ms, NEX = 2, FOV = 24 cm, matrix = 224 × 224, and 4- to 5-mm slice thickness. In our experience, however, tissue contrast is not as good in PROPELLER sequences as in conventional spin-echo or STIR sequences. Our routine rapid acquisition MRI protocol acquires axial DWI images and then 2D HASTE images in orthogonal axial, sagittal, and coronal planes and does not use PROPELLER. For HASTE, we use TR/TE = 20,000/90 ms, NEX = 0.5, FOV = 24 cm, matrix = 256 × 256, and 4-mm slice thickness. As noted above, we have found that this short protocol can be effectively used to evaluate ventricular size in children with suspected shunt dysfunction.
A number of sequences have been developed to exploit contrast related to magnetic susceptibility, including T2*-weighted GRE, susceptibilityweighted imaging (SWI), and susceptibility-weighted angiography (SWAN). They share in common the use of short TR, long TE (25-50 ms) GRE acquisition, which sensitizes images to T2* contrast. The techniques differ in their use of 2D or 3D encoding, the application of flow compensation gradients to reduce flow artifacts and the approaches used to process the complex-valued MR measurements, which consist of two values—one representing magnitude and the other phase—for each voxel in an image.
The minute distortions in the magnetic field that are induced by paramagnetic or diamagnetic tissue components give rise to signal loss, or “blooming,” on magnitude images. These are often useful to identify for areas of old hemorrhage, as in suspected trauma or vascular malformations (63
). Beyond infancy, these images may sometimes also provide the only clue on MRI that calcification is present, for example within a brain tumor or as the result of congenital infection.
The phase component is ignored for most sequences, and only the magnitude component is used to construct the image. However, image phase in T2*-weighted images is linearly related to tissue magnetic susceptibility and can be exploited to visualize this information. Paramagnetic compounds such as hemosiderin or ferritin within hemorrhage or deoxyhemoglobin within veins cause a positive phase shift, whereas diamagnetic compounds such as calcium induce a negative phase shift. With SWI, phase information is added to the reconstructed image in order to heighten sensitivity to susceptibility effects. Phase images can also be viewed directly to help determine whether tissue is paramagnetic or diamagnetic and thereby differentiate between iron- and calcium-containing compounds. As 3D techniques, SWI and SWAN can take longer to acquire than conventional T2*-weighted GRE, but satisfactory resolution can usually be obtained in under 5 minutes. New versions that use echo-planar acquisition are being developed that should shorten the acquisition time (63
It should be emphasized that higher field strength increases sensitivity to susceptibility contrast, such that 3 T is more likely to reveal the presence of these tissue components than 1.5 T. 7 T MRI scanners, one of which has received conditional FDA approval at the time this chapter was written, permit greater susceptibility contrast and for this reason are likely to gain traction for clinical evaluation in certain indications in the near future.