H Micro-Imaging. Tuning and Matching. i. Open any 1H data set and type wobb.

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1 - 1-1 H Micro-Imaging The NMR-specific properties of the objects are visualized as multidimensional images. Translational motion can be observed and spectroscopic information can be spatially resolved. Tuning and Matching i. Open any 1H data set and type wobb. ii. The tuning and matching rods are located under the magnet. Since the magnet is set up to measure different nuclei, make sure to use the rod wrapped in yellow tape if the nucleus of interest is proton. iii. There are two ways to tell the status of tuning and matching. The computer screen shows the signal along a frequency scale. The goal of this process is to obtain the largest peak minimum which is centered around the red line marker. Changing the tuning and matching rods concurrently will provide the most successful results. There are also LED lights on the top of the HPPR unit that indicate the quality of tuning and matching. The same process of twisting both rods concurrently can be performed with the goal of getting the minimum number of lights displayed on the screen. A less-thansufficient tuning and matching job will produced yellow and possibly red LED lights. A sufficient tuning and matching job will produce one or two green lights on either side of the middle line. iv. Once the probe is tuned and matched, press (or type) stop.

2 - 2 - Shimming In many cases, there is a standard parameter set and experiment used for shimming protocols. The shims are often stored for each user and each type of sample they measure. Below is a list of useful commands for the shimming process. Rsh This command reads shims from a list of saved parameter sets. Type rsh, select the desired shim set, and press Ok. The message rsh:finished will appear at the bottom of the screen when the operation is complete. Wsh After shimming is complete, it is necessary to save the new shims. Type wsh, give a name for the new shim set, and press Write. Setshim Sometimes users prefer to type in the values of each shim direction rather than scrolling to it using the knob on the BSMS keyboard. This command recalls a complete list of the current shims and allows one to type in values. The water line here has a shoulder The water line here has better resolution

3 - 3 - The zg Experiment zg is both the name of a pulse sequence and a software command. The command zg means instructs the software to perform an acquisition on the current dataset. The pulse sequence entitled zg is a simple one pulse sequence in which the magnetization is excited by a rf pulse and observed. Often parameters need to be optimized for the sample such as D1 (related to the T1 NMR relaxation of the sample) and P1 (rf pulse corresponding to a 90º tip angle). The signal obtained from a zg sequence can be used to check that the hardware/software is functioning properly, that shimming is optimized, and the quality of the sample is sufficient. It is customary to do zg experiments on samples with the same set of parameters before and throughout each measurement to check for consistency. Figure 1. Schematic of zg sequence. Experimental Procedures a. Open a zg sequence. b. NS the number of scan is usually determined by the phase cycle of the particular sequence. c. SWH/DW/AQ/TD the spectral width (SW) is the width of the spectral window which is determined by the sampling rate. DW is the dwell time which is the time period between two successive data points recorded by the software. For the fixed number of data points (TD) acquired by the spectrometer the following rule applies: the larger is the DW, the smaller is the SWH. AQ is the acquisition time of the experiment. AQ should be chosen in such a way that the fid is equal to (for maximum signal-to-noise) or be shorter than ¾ of the AQ time. Fid duration can be estimated by looking at the time domain signal. Check this by running the experiment and verifying in the FID tab. If the AQ is too short, not all of the FID will be recorded. The latter might lead to

4 - 4 - measurement artifacts. If the AQ is too long, there will be a larger contribution from noise to the signal. TD - the number of data points collected during acquisition. SWH, DW, AQ and TD are all related and should be adjusted concurrently. d. D1 this delay should be 3-5 times larger than the T1 relaxation time. T1 relaxation values can be determined using the inversion recovery sequence described later in the manual. e. P1/Pl1 The Pl1 value is the power level for the rf pulse and is usually set to 0 db and P1 is determined by doing a P90 optimization experiment described in the next section. f. RG receiver gain can be automatically determined after all other parameters have been set by typing rga. ii. Type zg to run the experiment. The experiment can be observed in real time by selecting the Acqu tab and opening that window. Processing the data i. In order to convert the time-domain signal, or the FID, into frequencydomain spectra, a Fourier transform in required. The command ef will perform exponential multiplication and Fourier transform. ii. Phase correction can be performed automatically using a number of commands as well as manually. The command pk will perform automatic phase correction using the current values of PHC0 and PHC1 which are the zeroth and first order phase correction values stored in the ProcPar tab of the dataset. The command apk will calculate these values and use them to correct the phase. The command mc will apply a magnitude calculation for phase correction. Use PH_mod to set the mode for automatic phase correction. This can also be found in the ProcPar tab window. In order to manually perform phase correction, click the button in the top toolbar and a new window will open. In this new window, there are two buttons which can be used for zeroth and first order phase correction. Set the center line at the middle of the NMR line of interest using the right mouse button. Click and hold the zeroth order button and use the mouse to correct the phase. The first order button can be used further in the same way. Then press the save button to store the correction. *If doing phase correction on a spectrum which is part of a 2D dataset, click on the Save to 2D button to save these phase correction parameters for each spectrum in the set.

5 - 5 - P1 Determination The optimization of 90 radiofrequency pulses is performed using an AU program entitled paropt. This program can optimize a number of parameters by conducting a series of experiment using the chosen pulse sequence modifying one parameter of choice and choosing the optimal value according to the input regulations. In the case of P90 optimization, the program should be told to choose the value of P1 (the duration of the rf pulse intended to be 90 ) which gives the maximum signal. Experimental Procedures i. Open a zg data set with appropriate parameters for the given sample. ii. iii. Run and process the data set as normal. Type paropt iv. Choose to modify the parameter P1. v. Select the range (minimum and maximum) and/or the number of increments. vi. The paropt program will give a set of FID s. If Figure 2. Example of P1 optimization experiment indication the different pulse lengths along the time scale (in μs)

6 - 6 - Determination of NMR Relaxation Times T 1 inversion recovery The inversion recovery sequence ( t1ir1d ) is a standard pulse sequence used to measure the T1 NMR relaxation time. The sequence consists of a 180 rf pulse which tips the magnetization into the z-axis followed by a duration τ and a 90 rf pulse which tips the magnetization into the transverse plan where the signal is acquired. T1 NMR relaxation occurs during the τ time period which causes attenuation of the signal measured at the end of the sequence. By varying this time period and observing the attenuation behavior, information about the T1 NMR relaxation time can be determined. The value of D7 at which the signal is zero (tinv) and the T1 relaxation of the line under observation are related by T1 t inv ln 2 Figure 3. Schematic of inversion recovery pulse sequence (t1ir1d).

7 - 7 - Getting Started in Paravision 1. Create a new study in Paravision 6 2. Drag and drop a SINGLEPULSE experiment to the active window and click Continue 3. Choose a Localizer experiment to verify the sample is in the correct position, click Continue Quality Control Calibration of XYZ Lego phantom pre-emphasis, ECC, B0 Spin-Echo Image S/N ROI measurement DTI Calibration with tridecane Select the DTIstandard experiment and 6 directions, click Continue Ultrashort Echo time experiments Select UTE, select 3D and click Continue Zero Echo time experiments Select ZTE and click Continue