This research was performed at the Glasgow Experimental MRI Centre (GEMRIC) on a Bruker Avance Biospin animal scanner with a 7 Tesla magnet with a 15 cm RF coil and a bore size of 152 cm. In order to determine the best parameters for the 3D scans, a pre-scan was run as well as a short, localizer tripilot scan which helps to make sure the column is placed in the most precise position possible between experiments. To obtain the high resolution clean and biofilm scans, a 3- dimensional rapid acquisition relaxation enhanced (RARE) sequence with a resolution of 300àm across the x- y- and z- planes was used to excite the 1H
Peristaltic pump Influent Cu
Influent tubing Effluent tubing to waste
View of column in MRI bore
Bore with plastic tube MRI System
(magnet & coil)
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nuclei within the sample and thus, image and determine the water and non- water phases of the gravel column. The RARE scan consisted of a train of RF pulses 90ox [-te -180oy –te -]n with an echo time (te) of 11 ms, a RARE factor of n = 8, a repetition time of 4000 ms and a bandwidth set to 200 kHz. While higher resolution scans are possible, this increases the scan time and with the parameters utilized in these 3D scans totalling 20-21 hours, is already sufficiently high. 3D images consisted of 600 vertical slices which are 333 pixels high and 433 pixels wide (Fig 4.10).
Figure 4.10. Orthogonal directions of x, y and z and examples of resulting images obtained from the 3D acquisition
This sequence and setup has been successfully utilized to image gravel sedimentation in Haynes et al. (2009) and was thus used without modification in this study. Since this MR system utilizes a more powerful superconducting 7T magnet for a higher strength magnetic field than typical medical MR, images acquired are more susceptible to distortions or artefacts. Optimized image quality has been augmented with previous work of determining a low metal gravel lithology suitable for MRI use in Haynes et al. (2009); Ramanan et al.
(2012) and Haynes et al. (2012) as well as chamber construction and experimental setup by Minto (2013). Thus, the MR images obtained were free from possible distortions due ferromagnetic artefacts or wrap-around effect.
Though images obtained did experience gradient non-linearity near the outlet end resulting in a tapering effect in the image (Figure 4.11) as well as intensity inhomogeneity in which signal intensity across the image varies. To address both issues: Firstly, gradient non-linearity was removed for the high resolution 3D
433 pixels
333 pixels
Y vertical Slice x 600 (left to right)
Z horizontal slice x 433 (top to bottom)
X Z
Y
Column
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scans by the analysed area being reduced from the original 600 Y slices to the 152 Y slices free of non-linearity distortion (Figure 4.11). This reduced volume was utilized for further processing of porosity data. It is important to note that each Y slice is 88604 pixels, hence even the reduced volume space from 152 slices still contained over 13 million pixels with associated complexity and lengthy analysis requirements. Secondly, intensity inhomogeneity was addressed through utilization of binary processing (described in Section 4.2.7); this is viable as Figure 4.11 indicates that this affects the blue/green wavelengths of the colour spectrum of the fluid signal only; distinction of the solid-fluid boundaries remains clear and thus binary processing can be accurately utilised.
Figure 4.11. Example of horizontal Z slice (433 total from top to bottom) from the 3D high resolution scans. Non-linearity can be seen tapering near the outlet end and the different colors show the intensity inhomogeneity. The area between the green lines indicates the useable portion for image processing the porosity and comparison and equals 152 slices vertical Y slices out of the total 600 obtained.
The clean and biofilm scans were run as 3D high resolution scans in order to determine porosity of the gravel and look at possible biofilm growth between the two. Care was taken to match up the scans when placing the column within the MRI after growth periods and was done so with alignment points on the column, the MRI system and the plastic bore as well as comparing between the initial tripilot scans, ensuring the column was imaging in the same location
Non-linearity = tapering Intensity inhomogeneity = different colors
Useable portion = 152/600 Y slices
Inlet Flow Outlet
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between the Clean and Bio scans. Once the biofilm scan for the ‘Bio’
experiments and the clean scan for the ‘Chem’ experiments was run, the flow scans were run immediately after without movement from the MRI system.
As the high resolution 3D scans took 20 hours to complete (Clean and Bio scans) the flow rate and diffusion/advection of Cu tracer through the column required a far quicker image acquisition time so as to ensure multiple images of tracer movement. With the aim to run a scan frequency of 5 minutes, a maximum scan acquisition timeframe of 2 minutes was chosen as an appropriate compromise for process understanding and MRI set-up. This reduced the number of image slices to 8 horizontal slices through the column (from top to bottom) as visualized in Figure 4.12. Between 12 and 24 scans were taken for time-lapse imaging of tracer movement. Thus, the resulting imaging parameters were set up for the flow experiments; 440 àm resolution, echo time (TE) 170.5 ms, repetition time (TR) 24000 ms, a RARE factor of 48, the field of view was 11 cm with an imaging matrix of 250 x 250 pixels and an 8 pixel slice thickness.
Figure 4.12. (a) Photo of the gravel filter column with inlet on the left and outlet on the right, and thus flow applied left to right (b) schematic of the 8 horizontal slices for each flow scan obtained (c) resulting MRI image of once slice