Multi-planar Reconstructions in Routine Applications Greg Brown 1997
This paper will briefly re-introduce the central concepts of 3DFT scanning and MPR, examining the factors affecting image quality and the manipulation of SNR. It will describe the sequences we have found most effective for a range of examinations, and suggest further developments.

What is Multi-Planar Reconstruction ? (MPR)
What Can MPR be used for ?
MPR Image Quality Issues
3DFT Acquisition Principles
3D Raw Data & K-Space
Non-Selective Vs. Selective 3D
RF Pulses & Slice Profile
Manipulating 3DFT SNR
Artefacts in 3DFT
3DFT Data Handling
3DFT Sequence Types
Practical Applications
Isotropic T1 weighted Brain Imaging
Siemens Solution T1 MP-RAGE
GE Solution IRprepped FSPGR
High Resolution Brainstem Imaging
Interactive Examinations
Scoliotic Spine


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While there is nothing conceptually new about 3DFT and MPR, recent developments of commercial hardware capability and sequences now make them practical and easy to implement. In MRI now is always a good time for change. This paper aims to get you to make that change.

The installation of a replacement MRI scanner at the Royal Adelaide Hospital offered the opportunity to review and adapt virtually all aspects of MRI technique. Fast Spin Echo (FSE or TSE) phased array coils, and stronger gradient systems allowed substantial improvement in image resolution, particularly in spine, joint and T2 weighted brain imaging. In seeking a solution to thinner slices and higher resolution for T1 weighted brain imaging, 3DFT sequences and Multi-planar Reconstruction (MPR) were employed. Once the step of using 3D sequences and MPR was taken, we found a range of practical 3DFT sequences suitable for exploiting MPR as a daily standard technique tool in clinical applications. It is particularly applied where more conventional approaches have reached their limits of speed or resolution, where the anatomy under examination requires complex and curved plane display, or where multiple plane examinations make 2D acquisition inefficient.
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What is Multi-Planar Reconstruction?
Voxel shapes

Multi-planar reconstruction (MPR) software re-formats images at arbitrary planes, defined by the operator, using the pixel data from a stack of planar images (base images).
The digital value for each pixel is assigned to a virtual voxel with the same thickness as the slice thickness of the base image. This yields a volume of data that represents the scanned object. The MPR software uses the virtual voxel data to create the pixel values for the reconstructed images. When the dimensions of the scanned voxels (as set by slice thickness and in-plane resolution) are equal, the data set is said to be isotropic. Where the dimensions of the scanned voxel are not equal in all three planes, the data set is said to be anisotropic. Isotropic data yields the best reconstructions.
When applied to CT and MRI data the MPR images can aid perception of anatomy by providing a perspective or display not seen in the base images.
MPR software typically uses an interactive interface that allows the user to prescribe the reconstruction planes and parameters from simple reconstructed images, in a manner analogous to scanning the real patient. The user can select plane orientation and thickness (typically equal or greater than the base scan thickness), and can prescribe the number, location, and separation of reconstructed slices. Individual MPR programmes have their own sets of rules and constraints for data input which can at times place limitations on the parameter choices in the base sequences. Of greatest importance is the number of data points allowable (slices* matrix), which will largely be a function of computer memory. This limit is rarely expressed explicitly but will be encountered with adventurous sequence development. Most MPR software can accept 2D slice data, and can accommodate some slice gaps.
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What can MPR be used for?

Once suitable base scans have been performed, we have a tool to "virtually" scan the patient without further need to keep them in the scanner. The base scan data can be used to create images precisely aligned with anatomical planes, create sets of slices with multiple orientations and slice thicknesses (at the same contrast weighting as the base scans), interactively roam through anatomy, and compensate for positioning errors.
The MPR technique is an accessible tool that can replace or complement more conventional imaging approaches. MPR can be routinely used in examinations of the CP angles and cranial nerves, pituitary gland, solitary and multiple space occupying lesions of the brain, in the knee joint, and for examining the kypho-scoliotic spine.
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MPR Image Quality

The quality and utility of MPR images is directly related to the quality of the base images used to create them. In this sense the factors affecting image quality are the same as for any scan. Suitable contrast, SNR, contrast to noise ratio (CNR) and the minimisation of artefacts are most important. Because most MPR work involves the use of short TR GRE 3DFT sequences, obtaining suitable image contrast can be difficult. As will be discussed later, the best solutions are offered by complex and efficient GRE sequences.
Geometric parameters assume an added importance in this application. Slice thickness cannot be used to provide SNR to compensate for losses inherent in providing high in-plane resolution. Optimum results require slice thickness equal to the in-plane pixel size (isotropic data). When the data is not isotropic, images reformatted using the larger dimension will show reduced spatial resolution. This problem is worst when the large dimension is in the reconstruction plane, but its visibility will depend on the level of anatomical detail that needs to be resolved.
Artefacts causing geometric distortion of the base image will also degrade the MPR image fidelity. Contrast and signal loss from cross talk becomes a problem when designing thin slice contiguous 2DFT sequences, particularly in multi-slice sequences with low acquisition bandwidths. While attempting to maintain a reasonable number of slices per unit TR, the sequence designer may choose a shorter period RF pulse, to make up for the increased sampling time dictated by a low acquisition bandwidth, sacrificing pulse shaping and slice profile in the process.
The MPR software will employ specific algorithms to assign the pixel values of a reformatted slice. The image quality will depend on how well these handle multiple voxel values in thick slices, and how the data gaps resulting from inter-slice gaps are interpolated. The interpolation routines of magnification programmes can also significantly affect presented image quality.
In any given system best results are obtained with small dimension isotropic data sets acquired from 3DFT data. When using 2DFT sequences, keep slice thickness and slice gap as small as possible, and plan to reconstruct planes at small angles to the acquired plane.

For best results use (in order of preference):

High SNR sequences with a: - 3DFT small dimension isotropic data
3DFT small dimension anisotropic data
2DFT thin slices with minimal or no inter-slice gap and optimised slice profile.
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3DFT Image Acquisition

3DFT is a spatial encoding regime that can be applied to virtually any excitation sequence. It is also referred to as 3D, or Volume acquisition. 3DFT sequences still generate two dimensional images in the acquisition plane; they differ from 2D acquired sequences in that the MR signal is generated from the entire imaged volume, rather than the individual imaged slices. For any given image thickness, the 3D sequences use lower gradient strengths than 2DFT.

Figure 2 shows a pulse-timing diagram for a slice selective GRE 3DFT sequence.

The volume of tissue to be imaged can be specified by using the same technique as slice selective 2D imaging, ie. an RF pulse with a controlled bandwidth is applied in conjunction with a slice select gradient (Gz-ss). This tissue volume is resolved into slices by applying a phase encoding gradient in the slice select direction (Gz-phase). The number of increments of Gz-phase equals the number of required partitions. The excited volume is called the SLAB or Slice, while the resolved slices are called PARTITIONS or Sub-Slices.

Usually Gz-phase is incremented through its full range of values while the Gy phase encoding gradient is held constant. The process is then repeated with the next increment of Gy phase.

For conventional sequences, 3DFT sequence time = .

3DFT GRE Pulse sequence diagram

 Incrementing Phase Encoding Gradients
The phase encoding gradient must be applied with a range of discrete values from
-Gmax to +Gmax to collect the required range of raw data. The number of steps determines the resolution in the phase encoding direction concerned. The maximum gradient strength (Gmax) determines the field of view in that direction. Low strength gradients, called the central steps (close to G=0), control the contrast of an image while the higher strength steps (+Gmax & -Gmax) are called the outside steps and determine the final resolution of the image. These titles refer to the locations in K-space that the phase encoding steps provide.

Sequence designers can employ a range of patterns to apply each of the gradient steps. These patterns are called the phase ordering. In sequential phase ordering, the gradient begins at -Gmax, stepping through G=0 to +Gmax (or vice versa). In centric phase ordering the central phase encoding steps are acquired first, progressing to the higher gradient steps in a balanced manner (+1,-1, +2,-2,+3,
-3....+Gmax, -Gmax). Other incrementation strategies are referred to as free phase ordering. A wide range of free phase ordering regimes have been designed to meet specific needs, of which the most common deal with respiratory or cardiac motion compensation.

Raw Data & K-Space
3DFT sequences generate three-dimensional raw data (Kx, Kz, Ky). It can be reasonably assumed that the nature of 3D K-space is similar to 2D K-space data. K-space trajectories are controlled by the spatial encoding regimes, particularly the phase ordering strategies, and the regions of K-space near the origin (low values of Kz, Ky) contribute most to image contrast. The data lines at higher values of Kz contribute spatial resolution of partitions, and the higher values of Ky contribute to in-plane resolution.

Non-Selective & Selective 3DFT
Some 3DFT sequences will operate with "hard" or non-selective RF pulses, in order to minimise TR. Others will be designed with selective RF pulses at the expense of minimum TR or bandwidth. When using a non-selective pulse the entire object should be included in the slab thickness to avoid aliasing of signals from outside the slab. A small FOV coil may also prevent this artefact.

Multi-slab 3DFT
When the TR must be long to provide the required contrast weighting multiple slabs can be excited in the same way that multiple slices are usually excited in 2DFT sequences.
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Manipulating 3DFT SNR

Because the signal is derived from the slab not the slice, the SNR of a 3DFT is significantly higher that a comparable 2DFT for a given volume of tissue. If we compare a multi-slice 2DFT sequence with a 3DFT sequence offering the same number of slices and thickness:-

equation Unfortunately scan time is proportional to Npartitions.
The SNR equations for 3DFT can appear complex but consideration of them reveals some key SNR handling tips.
The basic equation is:- equation
(BW = readout bandwidth expressed in Hertz/pixel)
The factors (FOV/ N) for x,y,&z express the voxel volume or spatial resolution of the sequence. SNR is proportional to root Nbecause there are Nz repeats of the sequence, for each of the different value of Gz-phase. Changing either Nz or Ny will affect spatial resolution (voxel volume) unless we are considering phase over-sampling in either direction.
Apart from coil selection, sequence bandwidth reduction offers the most efficient means of increasing SNR.
When all other factors are fixed equation. The individual dimensions of the voxel can be exchanged without affecting SNR. Any sequence designed with NEX greater than 1 can be re-configured by reducing slab thickness, and the number of partitions, to yield a 1 NEX solution with the same scan time, SNR and spatial resolution. In practice this can be used to deal with data overload of the MPR software as long as the sequence is slice selective and the required anatomy can be covered by the reduced slab size. This also explains why selective sequences are not faster than non-selective sequences, unless they offer shorter TR for the same or acceptable image contrast.
If the bandwidth and spatial resolution are set, all other attempts to improve SNR come with a heavy time penalty. The number of acquisitions (NEX) and phase encoding over-sampling in the Y and Z directions will all provide SNR gains proportional to the square root of the time increase. This implies that all three factors can be traded off against one another to achieve different combinations with equal SNR and time.
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RF Pulse Shapes & Slice Profiles

In non-selective excitation, the slice select gradient isn't applied so the entire patient resonates at a single frequency, and a fast broadband RF pulse will excite all tissues within in the transmit coil. For slice selective excitation the SS gradient dictates that the resonant frequency will vary continuously along the slice direction. To achieve a rectangular slice profile the RF pulse must contain only those frequencies that equal the Larmor frequencies of the tissue in the selected slice location and thickness. Uniform excitation of the slice requires equal amplitude for all frequencies in the excitation bandwidth. In theory a pulse which contains a specific range of frequencies at equal amplitude would be infinitely long. In practice reasonable slice profiles are achieved with a pulse period of 8-16 cycles, but the longer the better.
Therefore the broadband excitation pulse suitable for non-selective excitation can be applied in less time than a well controlled narrow band pulse needed to achieve selective excitation. 

Artefacts in 3DFT
Any artefact that can affect a 2D image can affect a 3D image in the same way, although they can appear differently due to the difference in spatial localisation method. The phase encoding for partitions is prone to the same motion ghosts as normal in-plane phase encoding, but they will extend in the slice select direction and be noted on adjacent images. These can be seen across the slice select direction so the ghosts of the pulsatile object may not appear in the same slice as the artefact, nor in every slice. In multi-slab 3DFT, ghosts in the slice select direction will be restricted to the slab containing the source.
Aliasing is common in the slice select direction whenever the object is larger than the slab width. The signals from outside one edge of the slab will wrap around to the slices at the opposite edge of the slab. This is commonly seen as extra ears on sagittal head slabs, or bilateral display of the fibulae in knee sequences. Restricted view coils can minimise this aliasing. Phase over-sampling in the slice select direction is more effective but costs time.
The profile of the slab is prone to the same distortions as 2DFT slice profiles, and the poor slice profile common to many short TR selective 3DFT sequences is frequently seen. Edge slices will appear with poor signal level and little contrast. The severity of the effect depends entirely on sequence design and needs to be assessed individually. Its appearance is often compounded by slice direction aliasing. It is overcome by extending the thickness of the slab by 10-30%, acquiring extra partitions and discarding the poor images.
The slice profile of a partition is rectangular, so there is no loss of contrast due to cross excitation (cross-talk) between partitions.
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3DFT Data Handling
Reconstruction times are longer than 2DFT sequences due to the extra Fourier Transform step. Actual reconstruction times will depend on the number of voxels in the 3D raw data set, and the Fourier transform algorithms supplied by the manufacturer. In older scanners the Fourier transformation algorithms work more efficiently when the number of phase encoding steps and partitions is a power of 2 (2,4,16,32,64,128,256,512). Selection options may reflect this.
3DFT sequences generate very large raw data sets. When using phased array coils the raw data volume is multiplied by the number of coil elements, and can exceed the data handling capacity of the scanner. This restricts some applications at present.
Handling large amounts of raw and image data efficiently requires high computer memory, multi-image screen display, and fast archive and image recall software. Current release scanners can handle the data from most 3DFT applications adequately although there is need for improvement.
At the Royal Adelaide Hospital, we currently archive the base data as well as all the reconstructed slices so that the images used to report the examination are available as well as the capacity to create further views. 

3DFT Sequence Types
The major challenge for 3DFT sequences is scan time. For whole object isotropic data sets approximately 160 partitions are required with about 200 phase encoding steps so scan time = TR*(32,000 to 43,000 mSec). To obtain scan times less than 10 minutes, TR must be kept short. As TR falls below 100 mSec low flip SE and GRE sequences generate very low signal levels and have a poor range of image contrasts. More efficient sequences such as Contrast prepared GRE, segmented K-space GRE, GRE, PSIF, CISS, and DESS offer practical combinations of contrast, SNR and scan time.
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Isotropic T1 Brain Imaging

Problem: Thin T1 images
Thickness 5 mm 4 mm 3 mm 2 mm 1 mm
SNR drop per change   20% 25% 33% 50%
NEX for equal SNR 2 3 6 13 50
Scan Time (minutes) 3:12 4:48 9:36 20:48 80:00
Many brain applications need thin slice T1 images, but there are few time efficient or effective solutions. Scan times rise rapidly when extra acquisitions are relied on to compensate the SNR losses inherent in thin slice 2DFT.

T1 weighted TSE scans using low turbo factors (ETL=3-5) display poor Grey/White matter contrast. T2 decay induced blurring and ghosting are also significant problems. Turbo IR (FIR) sequences can use higher ETL (7-9) to yield good T1 weighting, but they offer limited slices and use very long TR. Their application is limited by scan time when very thin slices are required.

Conventional spoiled GRE can reduce TR by a factor of 5, to about 100 mSec, but the possible number of slices per unit TR demand multiple sequences (packets or packages) to achieve coverage. 3DFT spoiled GRE with TR near 100 mSec, overcomes the slice limits, but the scan times are still very long.

Low bandwidth sequences used to compensate low SNR, require longer data acquisition times, reducing the number of slices per unit TR. Attempts to recover this lost time by reducing the period of the RF pulse result in poor slice profiles and more cross-talk. (see RF Pulse Shapes & Slice Profiles)
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Siemens Solution: T1 weight MP-RAGE

MP-RAGE stands for Magnetisation Prepared RApid Gradient Echo. MP-RAGE is a 3DFT contrast prepared gradient echo sequence. The T1 weighted MP-RAGE uses a 1800 inversion pulse followed by a time delay (TI) to establish T1 contrast in the same manner as an Inversion Recovery (IR) sequence. As Mz evolves, the signal is acquired by a spoiled GRE sequence (Turbo-Flash) with a low flip angle and extremely short TR.

MP-RAGE uses sequential ordering of the in-plane (Gy) and slice select (Gz-phase) phase encoding. All Gz-phase encoding lines are collected following the contrast preparation pulse. The process is then repeated for the next value of the Gy phase encoding gradient. This strategy gives the shortest scan time as the number of partitions (Gz-phase steps) is usually smaller than the number of Gy phase encoding steps. Each Kyz line of data has a different contrast weighting as it is collected at a different period after the inversion pulse. The sequence contrast is dictated by the effective Inversion Time (TIeff) which is the time elapsed between the inversion pulse and the collection of the central Gz-phase steps (Ky fixed, Kx changing, Kz near 0). The 2DFT implementation of MR-RAGE is called contrast prepared Turbo-Flash.

Isotropic T1 MP-RAGE

The Siemens suggested protocol for MP-RAGE has been modified at many sites to provide isotropic 1 mm resolution. In the versions we currently use, the inversion and excitation pulses are not slice selective so the whole object must be included in the field of view. MP-RAGE sequences are available with longer TR and slice selective pulses, but in practice the sequence times are virtually equal for a given pixel volume. (See Manipulating 3DFT SNR). The sequence exhibits strong T1 weighting which is best appreciated on narrow window setting (use slow window control). Its high bandwidth masks susceptibility effects and keeps artefacts from dental and other metal very small. There is significant flow related enhancement in the inferior 2/3 of the images which allows MIP MRA images of the carotids to about the trunk of the middle cerebral artery. This drop-off of signal is due to progressive saturation of blood as it stays in the slab for successive excitations, and so the display of vessels would be better post contrast. Bright and dark pulsatile ghost artefacts result from flow in the internal carotid and basilar arteries. They are seen typically in the brainstem and cerebellum although not only in the sagittal partitions that contain the vessels. Eyeball motion is best controlled when the patient is scanned with their eyes closed. The sequence has good SNR so it can handle a 6/8 rectangular matrix. AP aliasing of the nose must be kept out of the posterior fossa. If phase over-sampling is used to control aliasing with the smaller matrix, remember that it may return the scan time to its original value. Keep an eye on the relative SNR indicator.
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Sequence parameters T1 Isotropic MP-RAGE
TR 9.7 mSec TE 4 mSec TI 300 mSec
TD 0 mSec Flip 120
Sagittal slab 160 mm 164 partitions
Frequency over-sampling, Phase A-P
100% 256 Matrix FOV 250 x 218 mm (7/8)
1 Acquisition Scan Time 7:05
Resolution 0.98 x 0.98 x 0.98 mm
Shim adjust before sequence

Characteristics of Isotropic MP-RAGE

Use MP-RAGE for T1 weighted images if the protocol requires: Or Clinical Applications of T1 MP-RAGE MP-RAGE Variants

Water Excitation MP-RAGE

The inversion pulses and excitation pulses are frequency selective for water protons therefore fat signal is virtually eliminated with a method suitable for post contrast applications. The slight increases in TR increase the scan time marginally. Because the fat signal is reduced by spectral methods rather than inversion, the sequence is suitable for use with Gd contrast agents. It is well suited to investigation of skull base tumours and optic nerve tumours, post contrast. The data set can be used to MIP angiograms of the major neck and cranial vessels with better results than the standard MP-RAGE.

Sequence parameters for Water Excitation MP-RAGE

TR 10.3 mSec TE 4 mSec TI 300 mSec
TD 0 mSec Flip 150
Sagittal slab 160 mm 160 partitions
Frequency over-sampling Phase A-P
100% 256 matrix FOV 250 mm (7/8)
1 Acquisition Scan time 8:25
Resolution 1 x 0.98 x 0.98 mm
Shim Adjust before sequences

MP-RAGE with gradient motion compensation
The gradient wave forms are designed to provide compensation of flow (GMR, Flow Comp), thus reducing the artefacts seen in brainstems from pulsating blood flow in the carotid and basilar arteries. This is particularly useful in children and post contrast where fat signal suppression is not needed. Fat and water are out of phase at 1.5T with this TE causing "Indian Ink" artefacts at the borders of fat and tissue. The Grey/White matter contrast is not as good, and the SNR is lower than the other MP-RAGE variants cited. The base images can be used to MIP angiograms of the major vessels with slightly better results than using water excitation variant, but the flowing spins reach saturation as they proceed up through the slab.

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GE Solution: IR prepped FSPGR
On a GE SIGNA 5.x system the 3D Fast Spoiled Grass sequence (3D-IR-FSPGR) with IR preparation is the nearest equivalent to the MP-RAGE technique. As with MP-RAGE, this sequence uses an inversion pulse followed by a spoiled low flip, short TR GRE train to collect all partition data (Kz), then repeating the process with a different value of Gy. The notable difference is that 3D-IR-FSPGR uses centric ordering of Gz. This means the selected TI is also the effective TI. The centric re-ordering strategy can lead to image blurring if a steady state is not achieved quickly with low flip angles (<20 degrees). In practice this requirement is not restrictive, and the images of the two sequences should look similar, but the TI parameters of the IR-FSPGR will be longer than that selected for MP-RAGE when achieving the same image contrast.

3D IR Prepped FSPGR
TR 20 mSec, Flip 25 degrees TE Minimum (bandwidth dependant)
TI 350 - 800 mSec (depending on Age)
Enhanced Dynamic Range ON
Sagittal or Coronal Slab 180 - 240 mm 3/4 FOV
Resolution approx 1 mm x 0.7 mm x 0.7 mm
Bandwidth less than +/- 10 kHz.
Michael Kean of Royal Childrens' Hospital, Melbourne, has optimised the sequence for general isotropic T1 weighted brain imaging. His parameters are shown in the technique box. The SNR of the sequence has been maximised by minimising the bandwidth. This protocol appears to display more extensive flow related enhancement (in children at least) than the MP-RAGE sequences.
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High Resolution Brainstem Imaging

CISS (Constructive Interference Steady State)
CISS is a strongly T2 weighted GRE sequence. In essence it is a pair of True FISP sequences acquired with differing regimes of alternating the phase of the excitation pulses. Individually these True FISP sequences display very strong T2 weighting but are affected by dark phase dispersion bands which are caused by patient induced local field inhomogeneities and made prominent by the relatively long TR used. The different excitation pulse regimes offset these bands in the two sequences. Combining the images results in a picture free of banding. The image combination is performed automatically after data collection, adding some time to the reconstruction process.
The overwhelming power of the 3D CISS sequence is its combination of high signal levels and extremely high spatial resolution. CISS images yield the best detail available of the cisternal portions of cranial nerves. In combination with the isotropic MP-RAGE we believe they completely remove any need for contrast media in identifying acoustic neuromas.
The sequence has inherent flow compensation because of its perfectly balanced gradients. Compared to conventional FISP or GRASS it is quite insensitive to CSF pulsations. True FISP and CISS sequences require a very high level of control over gradient switching and shaping. CISS requires very high local field homogeneity so an excellent base magnet homogeneity is required, and all sequences must be preceded with a patient specific shim adjustment. Metal in the field will degrade the images substantially so patient preparation should include the removal of all head and neck jewellery, and metal from clothing. CISS is available in 2DFT and 3DFT implementations.

Characteristics of 3D-CISS CISS in application
We currently use the parameters suggested by Siemens in the VISION VB25A software to provide a very high resolution anisotropic data set for imaging the CP angle and structures of the inner ear. This is not a novel approach but automatic combination of the images makes the technique easy to implement on a routine basis.
After acquiring the scan, put the slices into MPR software to create axial images properly aligned with the acoustic nerves. At these slice thicknesses perfect positioning is impossible and presentation is greatly enhanced by an anatomically correct display. For optimum display of the VII and VIII cranial nerves from brainstem to middle ear angle, angle upwards from transverse to coronal almost parallel to the roof of the 4th.

CISS Sequence parameters
TR 12.25 mSec TE 5.9 mSec Flip 700
1 transverse slab 32 mm thick 46 partitions
Matrix 230 x 512 (60%) 200 x 150 mm FOV
Frequency over-sampling Phase L-R
1 acquisitions Scan time 4 min 20 sec
Resolution 0.7 x 0.65 x 0.39
Patient shim before sequence

CISS Protocol Variations:
Imaging time can be reduced to 3 minutes and SNR improved by 20% by choosing a partition thickness of 1 mm. Display of the cisternal portions of cranial nerves is significantly better than can be achieved with TSE techniques, but the MIP reconstructions of inner ear structures are noticeably poorer.
By selecting 32 1 mm partitions, 1 NEX FOV 250 x 187 mm (6/8) with a 0.5 mm square pixel, the SNR is virtually equal to the initial sequence but scan time is reduced to 5 minutes. The images look as good as the 8 minute images but cannot be placed in the MPR software as they contain too many data points. They can be used where scan time is an issue. Another good compromise is that suggested by Siemens for orbit imaging, increasing voxel volume slightly to 0.7 x 0.78 x 0.39 mm, to create a single NEX sequence at 6:42 that can still be MIPed.
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Other Alternatives
CISS is currently unique to late model Siemens MRI systems but a number of other high resolution T2 weighted approaches have been reported.
Customised sequences were investigated by Dr Schmalbrock et al using single small coils and SIGNA 3x and 5x. They suggested spatial resolution of .5 x .5 x 1 mm was achievable with the standard gradient system, but concluded that substantial SNR improvements were needed, through the use of better coils and shorter TE. They proposed 3DGRASS (25/7 500) to yield isotropic 0.5 mm resolution in 14 minutes with a 3 inch (7.5 cm) surface coil.
More recent work by Lee et al used a standard GE SIGNA, a phased array of two 3 inch coils and a customised sequence. They have suggested an overlapping interleaved set of 2 mm 2D FSE scans (see box) to yield images that can be used in MIP software, but would also be suitable for creating near axial MPRs. The sequence uses a flip angle of 1600 to attempt to reduce blurring of the shorter T2 tissues.

T2 FSE sequence parameters (SIGNA)
FSE ETL=32 ESP 19 mSec
3 sequences with 5 slices 2 mm thick interleaved to yield one slice each 1 mm
TR 4000 mSec TE 100 mSec Flip 1600 6 NEX BW +/-32kHz
FOV 200x100 mm Matrix 512 x 512 In plane resolution approximately 0.2 mm x 0.4 mm
Scan time 3 min x 3
The same group has been developing a 1 mm 3DFSE T2 weighted sequence.
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Interactive Examinations
MPR software and a suitable sequence can be used to interactively review complex anatomy while preparing an examination report in a manner analogous to the review stage many Radiologists perform with Ultrasound. The interactive examination can clarify difficult appearances on the filmed images, or can be used as a solitary sequence with all images being prepared later from the base data. Currently we use this sort of sequence as an adjunct to 2DFT sequences of the knee, but the method is equally applicable to any peripheral joint. We are also developing the approach for spinal examinations.

Knee 3D FISP
3D transverse steady state sequences (FISP, GRASS, etc) have been used in the knee for many years. Our current sequence has anisotropic data because of a relatively thick partition. This restricts the quality of coronal and axial views but it still provides excellent display of the cruciate ligaments and menisci in near sagittal planes. The sequence is slice selective. Slice direction phase over-sampling is used to control aliasing. Its T1/T2 weighting provides good display of cartilage, muscle and ligaments. Meniscal tears and degeneration appear bright and the thin slices make extension to the articular surfaces easy to identify. The fat signal from marrow is not excessive. Bright fluid signal aids the identification of effusions and cystic collections.

TR 22 mSec TE 10 mSec Flip 400 Scan time 6:02
Sagittal slab 96 mm 64 partitions 30% slab over-sampling
FOV 160 x 160 mm 256 matrix 69% Frequency over-sampling
Phase H-F 25% Phase over-sampling
1 Acquisition scan time 6:02 Resolution 1.5 x 0.9 x 0.63 mm

Isotropic FISP ?
Converting the 3DFISP sequence above to 1 mm isotropic voxels would require a slab thickness of 112 mm with 112 partitions, no slice direction phase over-sampling, and a 100% matrix. The scan time would become 10:33 and the relative SNR drops to 61%. The options to recover the lost SNR include reducing bandwidth to 50 Hz/pixel, using a more efficient coil, or changing to a more efficient sequence type.

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DESS (Double Echo Steady State) was originally known as FADE. It collects both the gradient echoes acquired in FISP (S+) and PSIF (S-) sequences and combines them. This increases the signal efficiency sufficiently to allow isotropic knee imaging with reasonable scan times. Phase encoding gradients are balanced to maintain the transverse steady state signals. The frequency encoding gradient is left on for the period of both the echoes, and is incompletely balanced to avoid dark banding artefacts otherwise associated with long TR fully balanced steady state sequences.
The contrast of DESS is quite unique. There is a strong fluid signal but fat is bright and other soft tissues appear similar to the short TR FISP image.
The PSIF echo is very sensitive to motion but this is not a major problem in orthopaedic applications. The parameters suggested are an application, using the current Vision software, of work by Hardy et al to optimise SNR and contrast between cartilage and joint fluid. Hardy suggests better results will be achieved with a lower bandwidth.

DESS Knee Parameters

TR 26.7 mSec TE 9 mSec Flip 60 degrees
128 mm sagittal slab 128 partitions
Matrix 256 x 256 FOV 250 mm 5/8 Phase A-P
1 Acquisition Scan Time 9:08 Resolution 1 x 0.98 x 0.98 mm

Water Excitation 3D DESS
The water excitation variant gives very strong bone/cartilage contrast and can be helpful in identifying regions of chondro-malacia. This protocol is slice selective. Back to the Top
Interactive MPR Imaging of the Spine
With suitable T1 and T2 weighted isotropic sequences spinal examinations for gross pathology might be reduced to two sequences. In practice this approach has its difficulties. Phased array coils multiply the volume of raw data by the number of coil elements used, so when combined with the high number of partitions required for isotropic imaging the scanner memory can easily be overloaded. The reconstruction time of phased array data is also extended and may become unmanageable with some 3DFT parameters. The quality and resolution available in phased array spine images has raised the standard. Radiologists may no longer be willing to accept 1 mm
in-plane resolution.
The resolution of the spinal cord within the complex curves of a kypho-scoliotic spine is the most obvious application for isotropic sequences and for the interactive examination approach. A suitable solution for that clinical picture would probably lead to more generalised and creative applications. At this stage we have not developed a T1 isotropic sequence, but we have applied a T2 solution.

T2 weighted 3D FSE
T2 isotropic acquisition can be achieved with multi-slab T2 weighted fast spin echo. The use of multiple slabs allows a low number of partitions and keeps scan time short. Two interleaved acquisitions are acquired to yield contiguous partitions. The MPR images can be aligned freely as the acquisition is virtually isotropic, but the resolution of about 1 mm may be too coarse for very subtle pathologies. Fat suppression should not be used in cases where a spinal lipoma may exist, nor should a posterior spatial saturation band. Patient movement between sequences can be a problem.

Sequence Parameters
TR 2800 mSec TE 120 mSec ETL 27 Flip 1600 - 1800
Sagittal 5 slices 8 mm Gap 100% 8 Partitions Slice select phase over-sampling 50%
Matrix 256x189 (98%) FOV 280x210 (6/8) Phase P-A Frequency over-sampling
1 Acquisition Repeat sequence with 8 mm shift
1 spatial saturation band anterior coronal
Resolution 1 x 1.11 x 1.09 mm Scan Time 3:58 (x2)

2DFT High Resolution FSE
2DFT sagittal spine slices are often put into a MPR programme to correct minor positioning errors. If the resolution of the 3DFT sequence is sufficient, the same approach can provide suitable images. Surprising results are obtained from 2DFT sequences with 3 to 4 mm slice thickness and high in-plane resolution (» 0.6 mm) as long as reconstructed images are not perpendicular to the acquisition plane. In most instances two or more 65 minute sequences are needed to provide sufficient coverage. They can be interleaved for contiguous coverage, avoiding crosstalk. Interslice gaps of up to 20% may not be noticeable but care must be taken to comply with the requirement of the MPR programme for handling inter-slice gaps. Typically this approach would only be used in the sagittal or coronal plane. Use your imagination.
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Special Thanks to:-
The Royal Adelaide Hospital MRI Staff Michael Kean    Senior MIT Royal Children’s Hospital Melbourne "MRI for Kids"
Trina White     MR Applications Specialist. Medical Applications
Mark Forth, Mark Harrison  GE Medical Systems Australia
Vicki Brown

1 Siemens Applications Guide I (Rev. 03 VB21C) Techniques Page B.4-12
2 Elster A.D. "Questions and Answers in Magnetic Resonance Imaging" Mosby St Louis 1994 ISBN 0-8016-7767-X
3.Wood M. In Stark D.,Bradley W.,"Magnetic Resonance Imaging" 2nd Edition Mosby Year Book St Louis 1992 ISBN 0-8016-4930-7
4. Ryberg JN, Hammond CA, Huston III J,Jack jnr CR, Grimms RC, Riederer S. T1-weighted MR Images of the Brain Using a Fast Inversion Recovery Pulse Sequence. JMRI 1966 6:356-362
5. Michael Kean Personal correspondence with author June 96. MRI Unit Royal Children's Hospital Flemington Rd. Parkville Victoria Australia Fax (613) 9345 5286
6. GE SIGNA Advantage Scan Reference Manual 2138249-100 Rev0 (Oct.95) Pp6-93 6-96. See also MR SIGNA Users' Newsletter
7. VB25A software Siemens Application Guide 2 (Rev. 04 VB25A). Protocols B.12-18
8. Siemens Application Guide 2. (Rev.04 VB25A) Protocols A.4-19 ciss3d_2_6b196.ykc see also pages B12-18, B.12-21
9. J Casselman, R,Kuhweide. M,Deimling, W.Ampe, I.Dehaene, L.Meeus Constructive Interference in Steady State- 3DFT MR Imaging of the Inner Ear and Cerebellopontine Angle. AJNR 14:47-57 Jan/Feb 1993
10. Siemens Application Guide 2 (Rev. 04 VB25A). Protocols B.12-21 t2_ciss_cor____new
11. Schmalbrock P, Brogan M, Chakeres D, Hacker V, Ying K, Cymer B. Optimization of sub-millimeter resolution MR Imaging Methods for the Inner Ear JMRI 1993 3:451-459
12. Lee JN, King BD, Parker DL, Buswell HR, Harnsberger HR. High Resolution 3D Imaging of the Inner Ear with a Modified Fast Spin Echo Pulse Sequence JMRI 1996 1:223-225
13. Harnsberger H.Ric Fast Spin Echo of the Temporal Bone Supporting notes 91-93 Second International Conference on Magnetic Resonance Imaging 5-9 April 1995 Melbourne Australia Dr. Oliver Hennesy St Vincent's Hospital Melbourne
14. Siemens Educational Update: Fast Steady-state Imaging: DESS, True FISP and CISS p2-3
15. Hardy PA, Recht MP, Piraino D, Thomasson D. Optimization of a Dual Echo Steady State (DESS) Free-Precession Sequence for Imaging Cartilage JMRI 1966 6:329-335
16. VB25A
17. Hardy PA et al, op cit 

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