Renal volumes can be calculated in several ways, using the ellipsoid formula or the voxel-count method. For the ellipsoid formula calculation, the length is determined on the sagittal scans. The width and thickness will be measured at the hilum on the transverse scans. Width can also be measured at the largest transverse diameter. Both volume-hilum and volume-maximum will be calculated. Volume
measurements using the ellipsoid formula can easily be done in less than 2 min. In most clinical studies, the ellipsoid method is commonly applied for renal volume
assessment. With this method, it is assumed that the kidney resembles an ellipsoid structure. This leads to systematic underestimation of the renal volume
. In fact the kidney is not a true ellipsoid structure.
With the voxel-count method, the volumes of all voxels within the boundary of the kidney are summated, thus giving the true total volume
of the kidney so that obtaining inaccurate results is highly unlikely. For the voxel-count method, the kidney has to be segmented manually. Segmentations can be done by tracing the boundaries of the kidney on each slice. The total renal volume
will then be calculated by summation of all voxel volumes lying within the boundaries of the kidney. Partial volume
effects, which occur if voxels contain both kidney and surrounding tissue, could lead to overestimation of the kidney volume
, if such voxels are included within the boundaries of the kidney. To avoid such an overestimation, the segmentation
line can be drawn halfway along the change in signal intensity between the kidney and surrounding tissues. Semiautomatic segmentation
techniques, such as region-growing, can save time. However, such methods are not really practical to use for most available software. Neighboring tissues with very similar signal intensity still have to be separated manually. Fat within the kidneys might perturb the segmentation
of the boundaries due to fat-water chemical shift artifacts when using region-growing segmentation
technique, leading to an underestimation of the total volume
. Semiautomatic segmentation
techniques are also challenging to perform on images obtained with accelerated T2 weighted MRI sequences. While accelerated T2 weighted imaging yields good results when organ morphology is considered, signal to noise ratio fluctuations between the individual slices due to spatial changes in the noise amplification intrinsic to parallel imaging techniques cannot be entirely prevented. For this reason, selection of threshold values and propagation has to be done individually for each slice and is a source for investigator bias and experimental error. Newer segmentation
techniques, like automatic contour detection, might be an option in future software implementations.
Calculating renal volume
from both coronal and sagittal scans can help eliminating differences due to aberrations in slice positioning.
Furthermore there is a simplified Mid-Slice Technique for MRI. In this technique, the renal volume
is calculated from the area of a single middle slice image of the kidney multiplied by the number of slices. The kidney volumes correlate well with stereology and have high reproducibility comparable with manual planimetry. However, when calculating single kidney volumes, both the mid-slice technique and the ellipsoid formula are less accurate than stereology and manual or semiautomatic planimetry. Although significantly faster than manual tracing for calculating kidney volume
, this technique is slower than the standard ellipsoid method. Volume
estimates are based on a multiplier linked to the hypothesis that the shape of the kidney is ellipsoidal.
All these approaches rely on geometrical assumptions, that might not be true.
3.1 MR Protocol Setup
3.1.1 Multislice Multiecho Sequence
for T2 Imaging
Load the 2D multislice multiecho sequence
(MSME). (preferred see Note 1)
Set the shortest echo time (TE) and echo spacing (ΔTE) possible, under the condition that fat and water are in phase (see Note 2). The last TE should be close to the largest expected T2(*) in the kidney multiplied by 1.5 (see Note 3). The aim is to acquire at least five echo images. Consider increasing the acquisition bandwidth and using half Fourier acceleration to shorten the first TE and ΔTE (see Note 4).
Choose the shortest possible repetition time (TR) for good signal-to-noise per time (SNR/t) efficiency. TR will be limited by the length of the echo train and the number of slices you acquire.
Adapt the flip angle (FA) to the TR and T1 in order to achieve the best possible SNR. Use the Ernst angle αE = arccos (exp (−TR/T1)) as a good starting value. Then try a few smaller and larger FAs and determine the optimal FA experimentally by comparing the measured SNRs.
Set a high acquisition bandwidth (BW) to shorten ΔTE, while keeping an eye on the SNR, which decreases with the square root of BW. Low SNR may be balanced out with averaging (see Note 5).
Enable fat saturation. On ultrahigh field systems this works well to avoid fat signal overlaying the kidney due to chemical shift. At lower field strengths it might work less efficient.
Enable the respiration trigger (per phase step or per slice). This is essential to reduce motion artifacts (see also Note 6), reduce motion blurring and unwanted intensities variations among the images acquired with different TEs.
Choose as phase-encoding direction the L-R direction and adapt the geometry so that the FOV in this direction includes the entire animal (approx. 40 mm).
Use frequency encoding in head-feet (rostral-caudal) direction to avoid severe aliasing. Adjust the FOV to your needs keeping in mind that in this direction the FOV can be smaller than the animal and a smaller FOV permits a smaller acquisition matrix, and in turn a shorter echo-spacing.
Use an appropriate slice thickness, typically around 1.0 mm.
Use high in-plane resolution that the SNR allows, typically between 100 and 200 μm. Zero-filling in phase encoding direction can be helpful to speed up acquisition. One may use half Fourier in read direction (asymmetric echo) to further shorten the first TE, if very short T2* (<5 ms) can occur. Reducing the excitation pulse length to below 1 ms would then also help to shorten TE.
A spin echo sequence
(MSME) with an echo time of >20 ms is very sensitive for instabilities of your system. If the system is not stable for any reason, this can often be observed directly at the time signal.
For examples of specific parameter sets please see Notes 9–13.
3.2 In Vivo MR Imaging
After obtaining scout images in the x, y, and z planes, T2-weighted MRI should be performed in sagittal and coronal orientation.
When selecting a certain type of MRI sequence
and its parameters, an optimum should be established between spatial resolution, signal-to-noise ratio, and scan duration. Accuracy of the volume
measurements can be enhanced by reducing slice thickness and/or choosing an additional section orientation transverse to the major axis of the kidney, mostly in axial orientation.
While theoretically beneficial for discrimination of kidney size differences, measurements in multiple orthogonal planes across the kidney prolong examination times and increase the time required for segmentation
, thus hampering both clinical and preclinical practice. This holds also true for application of sophisticated high resolution T2 weighted 3D imaging techniques instead of standard (multislice) 2D T2 weighted MRI covering the entire kidney. Especially in preclinical studies of diseased animals, it is often more appropriate to use solely a single slice orientation 2D MRI approach to gather standardized images in minimum time (i.e., to reduce length of anesthesia). If reduction of imaging time is of particular importance, accelerated imaging techniques are recommended. Such sequences should be available on all MRI systems. On Bruker systems they are identified by acronyms “RARE” or “turboRARE” (for rapid acquisition relaxation enhanced). On Siemens scanners such sequences usually are denoted “FSE” or “TSE” (for fast spin echo or turbo spin echo). In these measurement techniques acceleration is facilitated mainly by recording of multiple lines of k-space, that is, performing multiple phase-encoding steps on the echo train.
3.2.1 Scanner Adjustments and Anatomical Imaging
Acquire a fast pilot scan to obtain images in the three orthogonal planes x, y, and z.
Acquire anatomical images in several oblique orientations to facilitate planning a coronal slice orientation with regard to the long axis of the kidney, as described in the chapter by Pohlmann A et al. “Essential Practical Steps for MRI of the Kidney in Experimental Research.”
Perform localized shimming on the kidney as described in the chapter by Pohlmann A et al. “Essential Practical Steps for MRI of the Kidney in Experimental Research.”
3.2.2 Morphometric MR Imaging
Load the MSME sequence
, adapt the slice orientation to provide a coronal or axial view with respect to the kidney (in scanner coordinates this is double-oblique). (caveat see Note 8)
In the monitoring unit set the trigger delay so that the trigger starts at the beginning of the expiratory plateau (no chest or diaphragm motion) and the duration such that it covers the entire expiratory phase, that is, until just before inhalation starts (1/2 to 2/3 of breath-to-breath interval) (see Note 7).
Adapt TR to be a little shorter (about 100 ms) than the average respiration interval that is displayed on the physiological monitoring unit.
Run the MSME scan. Example images are shown in Figs. 2, 3, and 4.
A demonstration of the volume
changes that can be expected in pathophysiological scenarios is given in Fig. 4.