3.2 In Vivo MR Imaging

After obtaining scout images in the x, y, and z planes, a 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.

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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 the application of sophisticated high-resolution T2-weighted 3D imaging techniques instead of the 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 the length of anesthesia). If the 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 a 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

1. Acquire a fast pilot scan to obtain images in the three orthogonal planes x, y, and z.

3. Perform localized shimming on the kidney as described in the chapter by Pohlmann et al. “Essential Practical Steps for MRI of the Kidney in Experimental Research.”

1. Load the MSME sequence, and adapt the slice orientation to provide a coronal or axial view concerning the kidney (in scanner coordinates this is double-oblique). (caveat see Note 8) 

2. 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 the breath-to-breath interval) (see Note 7). 

3. Adapt TR to be a little shorter (about 100 ms) than the average respiration interval that is displayed on the physiological monitoring unit. 

4. 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.

4 Notes

1. A 3D version of the turboRARE sequence is also available, which allows thinner slices with better SNR but tends to be too slow for most in vivo applications.

2. The fat signal has a slightly different Larmor frequency (fat-water shift: Δf = 3.5 ppm ×Larmor frequency or 146 Hz/T, for example, Δf = 220 Hz at 1.5 T) than the water signal. The faster precession of the fat protons means that with increasing time the fat and water signal fractions within a voxel are sometimes in phase (signals add up) and some time out of phase (signals subtract). This can lead to an unwanted fat-water shift-induced signal intensity modulation along the exponential signal decay curve. This is mostly relevant for diseased kidneys with increased fat content (e.g., diabetes), but we recommend generally taking this into account, that is, also for healthy kidneys. The TEs at which fat and water are in phase depend on the field strength: TE [ms] = n ×(6.7069/B0[T]).

3. When establishing the MR technique you need to define an SNR acceptance threshold for the image with the shortest TE. The aim is to have at least three (better five or more) echoes with an SNR > 5. This threshold will depend on the expected T2 (*) values, which in turn depend on parameters like magnetic field strength, shim quality, and tissue properties (pathology). Example: For a rat imaged at 9.4 T using a four-element rat heart array receive surface RF coil together with a volume RF resonator for excitation in combination with interventions leading to strong hypoxia, an SNR > 60 was needed.

5. A good starting point is to use the same relative resolution as for rats. For this, reduce the FOV to the mouse body width and keep the matrix size the same. 

6. If no specific animal holder is used, it is preferable to position the animals in a left or right decubitus position to keep the bowels away from the kidneys to mitigate susceptibility artifacts. 

7. You must monitor the respiration continuously throughout the entire experiment and if necessary adapt the TR accordingly. 

8. Acquiring more echoes with smaller echo spacing will be bene- official because it improves the fitting when calculating a T2 map (see Fig.3), but keep in mind the specific absorption rate (SAR) associated with sending many 180° RF pulses in a short time could heat the tissue. This will usually not be detectable via a rectal temperature probe, but measurements with a temperature probe placed in the abdomen next to the kidney showed that signifificant temperature increases are possible with a multi-spin echo sequence.

9. Ellipsoid-based calculation: Example parameters for a 300 g rat at 9.4 T (Bruker small animal system): TR = [respiration interval] -100 ms; receiver bandwidth =50 kHz; the number of echoes =12; first echo =10.0 ms; echo spacing 10.0 ms; TE =10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120 ms; averages =1; slice orientation =coronal to the kidney; frequency encoding =head-feet; FOV =(38.2 ×48.5) mm; matrix size =169 ×115 zero-filled to 169 ×215; resolution =(0.226 ×0.421) mm; 1 slice with 1.4 mm thickness; fat suppression =on; respiration trigger =per slice; acquisition time =55–75 s (with triggering under urethane anesthesia).

11. Ellipsoid-based calculation: Example parameters for a 300 g rat at 3.0 T (Siemens Skyrafifit, a clinical system): Animal position: Right decubitus; Coil: Knee; TR =[respiration interval] ×500 ms; receiver bandwidth =399 Hz/pixel; the number of echoes= 12; first echo = 10.0 ms; echo spacing 10.0 ms; TE = 10, ..., 120 ms; averages =2; slice orientation =axial;  frequency encoding =left-right; FOV = (120x60) mm; matrix size = 256 × 128; resolution = (0.470 × 0.470) mm; 1 slice with 2.0 mm thickness; fat suppression = on; respiration trigger =off; acquisition time ~ 2 min. If no specific animal holder is used, it is preferable to position the animals in the left or right decubitus position to keep the bowels away from the kidneys to mitigate susceptibility artifacts.

12. Planimetry-based calculation: Example parameters for a 300 g rat at 9.4 T (Bruker small animal system): TR = 1700 ms; receiver bandwidth = 50 kHz; the number of echoes = 12; first echo = 10.0 ms; echo spacing 10.0 ms; TE = 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120 ms; averages = 1; slice orientation = coronal to the kidney; frequency encoding = head feet; FOV= (38.2× 48.5) mm; matrix size = 169 × 115 zero- filled to 169 × 215; resolution = (0.226×0.421) mm; 13 slices at 1 mm thickness; fat suppression = on; respiration trigger = per slice; acquisition time = 220–300 s (with triggering under isoflurane anesthesia). 

The following images should be acquired: coronal and transverse T2-weighted fast spin-echo sequence (TSE) and coronal T1-weighted TSE. 

The following images should be acquired: coronal and transverse T2-weighted fast spin-echo sequence (TSE) and coronal T1-weighted TSE. 

The parameters for coronal position TSE can be as follows: slice thickness, 2.0 mm; slice interval, 0.2 mm. 

For T1 weighted turbo spin-echo (TSE): repetition time (TR), 650 ms; echo time (TE), 10 ms; field of view (FOV), 120 mm × 120 mm; band width, 250 Hz/Px; matrix, 256 × 256; and several excitations (NEX), 4.0; 

For T2 weighted TSE you can use: TR, 3460 ms; TE, 35 ms; FOV, 120 mm × 120 mm; band width, 250 Hz/Px; matrix, 256 T×256; and NEX, 4.0.

The parameters for the transverse position T2 TSE can be as follows: slice thickness, 2.0 mm; slice interval, 0.2 mm; TR, 650 ms; TE, 10 ms; FOV, 120 mm × 120 mm; band width, 250 Hz/Px; matrix, 256 × 256; and NEX, 4.0.

Shimming is particularly important since macroscopic magnetic field inhomogeneities shorten T2*, but provide no tissue-specific information—rather they overshadow the microscopic T2* effects of interest and hinder quantitative intra- and intersubject comparisons. Shimming should be performed on a voxel enclosing only the kidney using either the default iterative shimming method or based on previously recorded field maps (recommended).

13. If the height-adjusted total kidney volume (HtTKV) must be calculated it can be done by measuring the kidneys in three axes. To calculate HtTKV a structural MRI or at least a CT scan is required. The height of the patient is also required for the calculation. The total kidney volume (TKV) is determined using an ellipsoid equation. This is clinically validated for patients with polycystic disease, with bilateral and diffuse small to medium-sized cysts. The ellipsoid equation requires only three measurements from both kidneys:

– Kidney length.

If you are viewing images on PACs or any DICOM-Viewer it is easiest to calculate the HtTKV with all planes of the kidney visible at the same time. To do this, you mostly have to select “MPR” under the available “View Options” in the specific menu. With this, you can view the kidney in the coronal, sagittal, and axial planes. The maximum length of the kidney should be measured in the sagittal plane.

Acknowledgments

This chapter is based upon work from COST Action PARENCHIMA, supported by European Cooperation in Science and Technology (COST). COST is a funding agency for research and innovation networks. COST Actions help connect research initiatives across Europe and enable scientists to enrich their ideas by sharing them with their peers. This boosts their research, career, and innovation.

PARENCHIMA is a community-driven Action in the COST program of the European Union, which unites more than 200 experts in renal MRI from 30 countries to improve the reproducibility and standardization of renal MRI biomarkers.

References

1. King BF, Reed JE, Bergstralh EJ, et al (2000) Quantification and longitudinal trends of kidney, renal cyst, and renal parenchyma volumes in autosomal dominant polycystic kidney disease. 11:1505–1511

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