Spectroscopy scan parameter selections

Select the appropriate scan plane. For Graphic Rx, remember that the STEAM CSI, Press CSI, PROBE-S, and PROBE-P voxels are prescribed in the same scan plane as the scan plane of the localizer images, while slices are prescribed orthogonal to the plane of the localizer images.

Select 2D to select a slice selective PSD. Select MRS to select a voxel localizing sequence.

The following Imaging Options are compatible with the spectroscopy pulse sequences:

• Extended Dynamic Range
• Cardiac Gating
• SSRF used with PROSE

Extended Dynamic Range is a recommended choice given the low signal common to spectroscopy data acquisitions.

The spectrum may be inverted. Make sure Extended Dynamic Range is turned on. If it is on and the spectrum is still inverted, correct the inversion in READY View : Adjust the Voxel shift procedure.

The echo time is used in six of the eight spectroscopy sequences. The FID CSI (MRS) sequence acquires an FID rather than an echo, so TE is not relevant. The Spin Echo (MRS) sequence has a fixed echo time of 2.5 ms, so the TE selection is not available.

The sequence repetition time. Since long repetition times lead to long exam times, the TR selection is often a compromise between acceptable signal loss due to saturation, and the length of the exam. For example, the minimum TR for the PRESS CSI and PROBE-P sequences is about 1.1 seconds while 5*T1 = 3 to 5 seconds for the common proton resonances in the human brain. A TR of 1.5 to 2.0 seconds provides a reasonable compromise between signal saturation at shorter TR values, and the increased patient examination times at longer TR values.

Auto Prescan always uses TR = 1500 ms, rather than the prescribed TR.

The nominal flip angle (power) of the RF excitation pulse in the Spin Echo (MRS) spectroscopy sequence. This parameter is inactive for the other spectroscopy sequences.

The FOV parameter determines the field-of-view along the frequency direction.

If Graphic Rx is used, the Slice Thickness or Voxel Thickness may not be available, and explicit entries may be required in the S/I, P/A, or R/L text boxes.

A CSI Slice Thickness entry may be required. The value is ignored just as in imaging scan prescriptions unless the signals from more than one slice are acquired or 3D CSI is performed.

Entries are always required for the S/I, P/A, or R/L text boxes. Entries and field names change depending on the pulse sequence, and on whether Graphic Rx is used to prescribe voxel or slice location.

The CSI Slices value should be 1, unless signals are actually being acquired from several slices or 3D CSI is performed.

The Table Delta field is ignored by all spectroscopy PSDs (set to 0.0 if an entry is required).

Frequency and Phase choices not only affect the data acquisition but they also determine the number of zero-fills applied during the reconstruction process, and the aspect ratios of the reconstructed images. The allowed Frequency and Phase values are 8, 10, 12, 14, 16, 18, 20, 22, and 24. No zero-fill is applied for the 8 and 16 selections, that is, the number of reconstructed CSI voxels is 8 or 16 along that dimension. The 10, 12, and 14 selections are zero-filled to 16, and the 18, 20, 22, and 24 selections are all zero-filled to 32 during the reconstruction.

Just as with standard imaging sequences, the default setting of the Freq DIR is usually the best choice. Swapping the phase and frequency directions, which for the voxel localized sequences has the effect of re-ordering (in time) the gradients used to define the voxel may help to eliminate artifacts.

Auto should be selected for all hydrogen spectroscopy acquisitions to insure that the water suppression pulses, saturation pulses, and slice selective pulses are transmitted at their correct frequencies. It should not be selected when acquiring signals from any other nuclei.

All spectroscopy raw data files are written to the system directory /usr/g/mrraw. There are two possible file types: standard system raw data files known as “P files;” and Spectroscopy Screen Save “P files.” Standard “P files” are automatically created and saved for all spectroscopy data acquisitions initiated with Scan from the Scan Operations screen. The Spectroscopy Screen Save “P files” are created and saved when the Save button is clicked on the Spectroscopy screen.

Generally, a raw data file consists of a raw file header, and one or more raw data frames; the number of data frames in a raw data file depends on the acquisition prescription and the acquisition technique.

When spectroscopy data sets are acquired, they are automatically saved to the /usr/g/mrraw directory. There are only 196 unique raw data “P file” names available. An existing file will be overwritten whenever a new file with the same name is saved.

• A “P file” name consists of the letter “P” followed by the five digit system run number, a period (.), and the number “7;” for example, P20480.7.
• The system run number is an integer multiple of 512 between 0 and 99,840 – there are only 196 unique run numbers, and therefore, only 196 unique raw data file names.

In its simplest form, a standard “P file” begins with a raw file header, followed immediately by a single baseline frame, and then by a number of raw data frames. The simplest form corresponds to the acquisition of spectroscopy data from a single slice or voxel with a single receive coil. On the other hand, a multi-slice data set contains the raw file header, a baseline and frames from the first slice, followed by the baseline and frames from the second slice, and so on to the baseline and frames from the last prescribed slice.

Similarly, data sets acquired using a phased array coil contain the raw file header followed by a baseline and frames from each of the active coils in the array. There are two types of raw spectroscopy data sets that can be acquired with Scan: Accumulate and CSI raw data sets.

• Accumulate: The number of raw data frames acquired and stored for each slice or coil in an Accumulate raw data set is determined by the values of two variables: Total Number of Scans User CV and NEX. Clearly the number of raw data frames is given by the quotient Total Number of Scans/NEX. The number of bytes in each frame (including the baseline frame) depends on the number of complex points in each excitation and the size of a data word, either 4 or 8 bytes. The size of a data word depends on whether the Extended Dynamic Range Imaging Option has been selected; 8 bytes if the option is selected and 4 bytes if not selected.

  For example, consider an Accumulate data set acquired using a four coil phased array with Number of Points = 1024, Total Number of Scans = 128, Extended Dynamic Range selected, and NEX = 2; there are 65 frames stored for each coil (128/2 + 1, remember the baseline frame), each data frame contains 1024 complex data points of 16384 bytes (= 2 * 8 * 1024), and a 61464 byte header. The size of the data set acquired from the four coils is therefore: (61464 + 4 * (16384 + 64 * 16384)) bytes = 4321304 bytes.

• Chemical Shift Imaging: A CSI data set consists of the raw file header, a baseline frame, and a number of frames equal to the total number of prescribed CSI phase encoding gradient amplitudes. The number of raw data frames stored for each slice or coil in a raw CSI data set is given by the product of the three CSI Resolution User CVs.

For example, if a 24*24 two-dimensional CSI data set is acquired with CV1 = 1024, and EDR is not selected, there are 577 raw data frames (24*24 + 1, remember the baseline frame). Each data frame contains 1024 complex data points of 8192 bytes (= 2 * 4 * 1024), and a 61464 byte header. The size of the data set is therefore: (61464 + 577 * 8192) bytes = 4788248 bytes.

The Spectroscopy Screen Save “P files” are created when you click the Save button on the Spectroscopy screen. Spectroscopy Screen Save file names start with the letter “P”, followed by the five digit run number, a period (.), the number “7”, another period, and two more numbers, usually two zeroes; for example, P10240.7.00. The “00” portion of the file name is used to differentiate files saved during or from the same acquisition. For example, if you acquired a data set and clicked Save to create the file P01024.7.00, and then clicked Save again without acquiring a new data set, the second file would be named P01024.7.01. As with the standard raw file names, there are only 196 unique Spectroscopy Screen Save file names, and existing files are overwritten by a new file with the same name.

A Spectroscopy Screen Save “P file” begins with a raw file header, followed immediately by at least one raw data frame – there is no baseline fame. A raw data frame is stored in the raw file for the signal acquired from each slice of a multi-slice acquisition, and/or for the signal acquired from each receive coil in a phased array coil set. The number of bytes in a raw data frame is determined by the Number of Points User CV, and by the Extended Dynamic Range Imaging Option. The number of data frames in a spectroscopy screen saved raw file depends on the number of prescribed slices and/or on the number of receive coils used to acquire the data. For example, the raw data file acquired from two slices with avg and Start on the Spectroscopy screen with the Number of Points = 2048, and Extended Dynamic Range not selected contains 94232 bytes (the 61464 byte raw file header, the 16384 byte data frame from the first slice, and then the 16384 byte frame from the second slice).

The spectroscopy pulse sequences can collect several different kinds of data sets:

• Images: The imaging mode, available with all the spectroscopy sequences, can be used to acquire image data sets. The images and the associated raw data sets are treated as standard imaging data; the raw data are discarded and the images are automatically added to the current patient exam.
• Averaged spectroscopy raw data: A single frame of averaged data is acquired and continuously displayed during all acquisitions initiated with the Start button on the Spectroscopy screen.
  • In the single1 Entry Point, the number of excitations equal to NEX is acquired, averaged into a single frame, displayed, and then discarded when the next frame has been acquired.
  • In the avg Entry Point, the number of excitations equal to the Total Number of Scans is acquired. During the acquisition, an updated average of the excitations acquired to that point is displayed every few seconds until all prescribed excitations have been collected and combined. The raw data must be explicitly saved with the Save button. Saved data are stored in the system directory /usr/g/mrraw as Spectroscopy Screen Save “P” files. The file names begin with the letter P, followed immediately by five numbers, a period (.), the number 7, another period, and two more numbers (usually zeroes); for example, P20480.7.00. The data in the raw data buffer used by the Spectroscopy screen processes are overwritten whenever the Start button is clicked.
• Chemical Shift Image raw data: CSI data sets are acquired from the Scan Operations area with the Scan button. If one of the CSI Resolution User CVs has been set to a value greater than one, a CSI raw data set will be acquired and automatically saved to the /usr/g/mrraw directory. Raw data files are stored as “P” files, e.g., P01024.7. Since there are only 196 unique file names, these files should be renamed and/or transferred to off-line storage. Each frame of a CSI data set is the combination of a number of excitations equal to the selected value of NEX. The number of raw data frames in the file is given by the product of the CSI resolution entries.
• Accumulate spectroscopy raw data: All non-CSI, spectroscopy data acquisitions initiated from the Scan Operations area with the Scan button are acquired and automatically saved to the /usr/g/mrraw directory. Each frame of data in an accumulate data set contains the number of excitations equal to the value of NEX. The number of raw data frames in the data set is equal to the quotient CV4/NEX. Raw data files are stored as “P” files, e.g., P01024.7.

Several simple spectroscopy prescription examples are presented to illustrate the data type and data acquisition concepts.

• Objective: Collect and store 64 excitations from one slice into a single, signal averaged, 2048 complex point data frame using the FID CSI (MRS) pulse sequence. Extended Dynamic Range is not selected.
• Prescription: Select the FID CSI (MRS) sequence, and on the User Control Variables screen, set the Number of Points = 2048, and the Total Number of Scans = 64.
• Acquisition: Click Spectro Prescan. On the Spectroscopy screen, enter avg in the Entry Point text box, and then click Start. When the acquisition is complete, click Save to store the raw data (as a Spectroscopy Screen Save “P file”) to the /usr/g/mrraw directory.
• Raw Data File: The raw data file contains the raw file header and a single raw data frame, a total of 77848 bytes (= 61464 + 16384).

• Objective: Use the PRESS CSI sequence to collect and store 128 excitations as 128 data frames each containing 2048 complex points.
• Prescription: Select the PRESS CSI sequence, and on the User Control Variables screen, set the Number of Points = 2048, and set the Total Number of Scans = 128. Select the Extended Dynamic Range option. Set NEX = 1.
• Acquisition: Click Scan. When the acquisition is complete, the raw data are automatically written as a “P file” to the /usr/g/mrraw directory.
• Raw Data File: The raw data file contains the raw file header, a baseline frame, and 128 raw data frames, a total of 4288536 bytes (= 61464 + 32768 + 128 * 32768).

• Objective: Use the PRESS CSI sequence to collect and store a two dimensional, 16 by 16 CSI raw data file from a slice in an axial scan plane. Where each of the 256 CSI data frames (each containing 512 complex points) is the average of 4 excitations, that is, each CSI phase encoding step is repeated 4 times.
• Prescription: Select the PRESS CSI sequence, and on the User Control Variables screen, set RL Resolution for CSI Scans = 16, AP Resolution for CSI Scans = 16, and SI Resolution for CSI Scans = 1. Select the Extended Dynamic Range option. Set NEX = 4.
• Acquisition: Click Scan. When the acquisition is complete, the raw data are automatically written as a “P file” to the /usr/g/mrraw directory.
• Raw Data File: The raw data file contains the raw file header, a baseline frame, and 256 raw data frames, a total of 2166808 bytes (= 61464 + 8192 + 256 * 8192).

All PSDs support Auto Prescan when acquiring proton spectra. To set the transmit power, click Auto Prescan. The APS process automatically adjusts the power level for the RF pulses specified in the data acquisition prescription.

The values returned by the APS processes for the Spin Echo (MRS) sequence are only approximations of the correct values. You should use the Spectroscopy screen tools to optimize and set the R1, R2, TG, and Center Frequency values.

APS is not supported for use with nuclei other than hydrogen; you must set the transmitter power (TG) manually. This is usually done by maximizing the signal level received while modifying TG. The single1 Entry Point with Start on the Spectroscopy screen should be used for this purpose – it may also be necessary to adjust the R1 and R2 receive gains while optimizing the transmit gain.

The frequency of the RF excitation pulses in the spectroscopy pulse sequences is set according to the value of the center frequency determined by the APS processes, or set to the value entered with the AX or DX commands on the Manual Prescan screen or the Spectroscopy screen. For the acquisition of hydrogen spectroscopy data, you should select Water in the Chem SAT menu; with this selection, the APS processes attempt to center the RF carrier frequency on the water peak in the spectrum. If the center frequency determined by APS is not centered on the frequency of the water resonance, the sequences may not behave as designed. The default settings of the RF pulses used for water suppression, spatial saturation, inversion recovery, and even excitation may require manual adjustment. The excitation, water suppression, saturation, and inversion recovery pulses are transmitted relative to the center frequency and may not be effective if the center frequency is not centered on the water resonance.

Excitation pulses in the FID CSI (MRS), Echo CSI (MRS), and Spin Echo (MRS) sequences are transmitted at the center frequency. For the STEAM CSI, PROBE-S, PRESS CSI, and PROBE-P sequences, the frequency of the slice selective RF pulses is offset from the center frequency by -128 Hz (an offset of about 2.00 PPM). This frequency offset minimizes chemical shift misregistration between the water localizer image or the voxel image, and the extremes of the observed frequency range in the spectra.

The spectroscopy pulse sequences use a variety of crafted RF pulses that were designed using the Shinnar-LeRoux algorithm. Where possible, the same pulses are used in different sequences to provide slice or voxel profile consistency. The RF pulses are designed to have a specific time-bandwidth product, which defines a fixed relationship between the width of the pulse and the effective bandwidth of the pulse.