Applications Guide for Interleaved 

Rephase/Dephase MRAV, 

Flow Compensated Double Echo 

SWI and SWIM 

  

 

 

 

Authors: Yongquan Ye, Ph.D. Dongmei Wu, MS.

Tested MAGNETOM Systems : 7TZ, TRIO a Tim System, Verio MR B15A (N4_VB15A_LATEST_20070519) MR B17A (N4_VB17A_LATEST_20090307_P8) 

Important Note: 

This document provides a description of techniques developed by MR facility, Wayne

State Univ (WSU), Detroit, MI, USA. This work-in-progress software has been tested

internally on our Verio, Tim Trio and Siemens-Bruker ClinScan 7T systems. However,

each user should be aware of the fact that incorrect use of this software may produce

unknown results. The sequences contained in this software package do not exceed the

FDA safety performance parameter guidelines for MRI exams. Specifically, there is no

change to patient risk as compared to routine operation of the MAGNETOM with regard

to: static magnetic field; the time rate of change of the gradient magnetic fields; the rate

at which RF power is deposited into the body (SAR); or the acoustic noise created by the

MAGNETOM.

The software has been tested internally but not yet in a clinical environment. For routine

applications, its functionality may not be complete, and use of this software will remain

investigational.

In general, the clinical user will, in its sole responsibility, decide on the use of this

application package or on subsequent therapeutic or diagnostic techniques and shall

apply such techniques in its sole responsibility.

WSU and the authors will not take responsibility for the correct application of, or

consequences arising from use of, this applications package.

The software in this package may change in the future, or may not be available in future

software versions. In case of any questions that are related to the use of this package

please contact one of the authors listed.

TableofContentsOverview .......................................................................................................................................... 4 

Sequence Description ...................................................................................................................... 5 

Sequence Installation ...................................................................................................................... 9 

Setting up Scanning Protocol .......................................................................................................... 9 

Image Examples ............................................................................................................................. 10 

 

OverviewThis package contains an extended variant of the 2D/3D GRE (Gradient Refocused Echo) sequence, which offers:

1) Simultaneous acquisition of TOF-MRA and SWI, i.e. MRAV; 2) Simultaneous acquisition of flow rephrased (FR) and flow dephased (FD) image

for enhanced MRA calculation; and 3) TR-interleaved mode for both 1) and 2).

By acquiring all data with a single scan, the motion induced image misregistration can be effectively removed. The focus of this package is to provide a means for simultaneous acquisition of MRAV images, including TOF-MRA and SWI as its basic function. Also since normal TOF-MRA has limited vessel-tissue contrast, we have developed and implemented a non-linear subtraction postprocessing method to selectively enhance artery-tissue contrast by additionally acquiring the FD data.

The final output of the sequence, depending on the selected imaging mode, may include the following images:

1) Two short TE flow compensated images, both magnitude and phase; 2) Long TE flow compensated images, including magnitude, filtered and unfiltered

phase images, SWI images and SWI mIP images; 3) Flow dephased dark blood images; 4) and finally from our processing: enhanced TOF-MRA images.

SequenceDescription

The interleaved rephase/dephase MRAV sequence is derived from the product a_gre sequence. Specifically, an ‘interleaved’ mode has been created to enable TR-interleaved acquisition of double echoes images with different flow rephase/dephase combinations, i.e. both echoes are flow rephased in TR1 while the second echo is flow dephased in TR2.

The diagram of the sequence is shown in Fig.1.

Fig.1 Diagram of the Interleaved Rephase/Dephase MRAV sequence. FR denotes flow rephase (i.e. flow compensation), and FD denotes flow dephase. In TR1, the two echoes are acquired with flow rephase gradients, and the TR2, the first echo is flow rephase while the second echo is flow dephase by a pair of bipolar gradients with low VENC value. TR1 and TR2 can be acquired in the same scan in an interleaved manner, or can be acquired separately, depending on the sequence mode selected.

Sequence mode

The sequence is implemented with 3 scanning modes: Interleaved, MRAV and enhanced MRA. The selection of the sequence mode can be found on the special card, as shown in Fig.2.

Interleaved: This mode obtains both MRAV and enhanced MRA results simultaneously, by acquiring the echoes in TR1 and TR2 in an

interleaved manner. Selecting this mode will double the scanning time relative to the other two modes.

MRAV: This mode obtains only the TR1 data without carrying out TR2 scans, and offers flow rephrased images with both short and long TE, respectively. The short TE images can be used as normal TOF MRA image, and the long TE images (both magnitude and phase) can be used for SWI calculation.

Enhanced MRA: This mode obtains only the TR2 data without carrying out TR1 scans, and offers flow rephrased images with short TE (TE1) and flow dephased images with long TE (TE2). Both images are processed using a non-linear subtraction method to enhanced artery-tissue contrast while minimizing vein-tissue contrast in the final images, thus giving an enhanced MRA image.

Fig. 2 Sequence mode selection, asymmetric echo setting, VENC gradient setting and phase high pass filter size.

Asymmetric readout

When asymmetric echo acquisition is set to ‘Allowed’ in Sequence->Part1, one can select the asymmetric factor and asymmetric echo type in the Special card. The schemes of both asymmetric echo type are shown in Fig. 3.

Original AsymEcho: This asymmetric echo mode is the same as what people have normally done and fills Kx partially with the echo center at the Kx center. The ‘AsymFactor Bef’ indicates the number of Kx points (in terms of the percentage of the whole Kx length) acquired before the echo center. Unacquired Kx points are zero filled. This

is the default mode that can be used in most cases. POCS partial Fourier reconstruction will be performed along RO direction if this mode is activated.

Extented AsymEcho: This asymmetric echo mode fills the whole Kx with shifted echo center. The ‘AsymFactor Bef’ is also defined as the number of Kx points (in terms of the percentage of the whole Kx length) acquired before the echo center. The echo center no longer coincides with the Kx center. This mode is designed for extremely high resolution imaging that exceeds the resolution limit of the scanner.

Fig.3 Schemes of original asymmetric echo and extended asymmetric echo acquisition.

 

VENC gradients (for flow dephasing) 

We used velocity encoding (VENC) gradients to achieve flow dephasing. Very low VENC values, 

e.g. ~1cm/s, should be used for best flow dephasing performance. According to VENC = 

/(2Gτ2), where G is the bipolar gradient amplitude and  the duration of echo gradient lobe, one needs a high G2 product for a low VENC value. We have set up the default values of G = 

24mT/m and = 4ms for a VENC value of 1.46cm/s. One can freely adjust both values via the 

Special card (Fig.2). 

The VENC gradients is implemented with the sequence mode of both ‘Interleaved’ and 

‘Enhanced MRA’. 

 

HP filter size 

This parameter sets the phase high pass filter size along RO direction for SWI processing. The 

filter size along PE direction is calculated as the product of this RO filter size and Nky/Nkx. 

 

VFA 

Variable flip angle. This is a testing parameter and is currently not used. Use the default ‘No’ 

option. 

 

 

SequenceInstallation1) .dll and .i86 sequence files    ‐>  C:\MedCom\MriCustomer\Seq\ 

2) IceProgramMRAV.evp      ‐>  C:\MedCom\MriCustomer\IceConfigurators\ 

3) MRAVConfigurator.dll +.evp    ‐>  C:\MedCom\bin\ 

4) libMRAVConfigurator.so    ‐>  C:\MedCom\MCIR\Med\lib\ 

5) Ctrl+Esc ‐> ’run’ ‐> type in ‘ideacmdtool’ ‐> select ‘PAS unload’ 

6) If the sequence cannot run due to ‘Image reconstruction’ error, restart image 

reconstruction via ‘System‐>Control‐>Image Reconstruction System card‐> Restart 

Image Calculation’. The restart only takes a few seconds, and the sequence would have 

recognized the ICE program. 

 

SettingupScanningProtocolSince the sequence is still under development, minor conflicts between protocol parameters may exist which will lead to certain parameters became unadjustable. This part will explain some tricks, which is actually simple and easy, to set up the protocol as desired without running into problems.

1) The contrast, i.e. echo number in each TR, is fixed to 2 for this sequence. The default sequence mode is 3D.

2) Turn on the flow compensation option for both echoes and set the high resolution as the first step. If the flow comp option is grey for the 2nd echo, try set the 2nd TE to a longer value first.

3) Set the desired slice thickness. 4) Set the desired FOV and RO bandwidth. 5) Set the desired TE after steps 2-4. If using ‘MRAV’ mode, use a smaller ‘VENC

Grad Duration’ in ‘sequence->special’ to achieve a shorter TE for the 2nd echo. This parameter is not in use for ‘MRAV’ mode so its value would not matter.

6) Enable SWI process, i.e. check the ‘SWI’ option in ‘contrast’->’common’ 7) Set the desired HP filter size via ‘sequence’->’special’. 8) Set all other parameters as desired.

 

ImageExamplesWith the SWI process enabled, the sequence will some or all of the following images depending on the sequence mode: 1) original magnitude images, 2) HP filtered and unfiltered phase images, 3) single slice and mIP of the SWI images, and 4) single slice enhanced MRA images. If the SWI process is not enabled, or 2D scanning mode is used, then only original magnitude and unfiltered phase images will be generated. Below are the examples of these images.

Magnitude (Echo11 & Echo 21, FR)

Magnitude (Echo12, FR)

Magnitude (Echo22, FD)

Magnitude MIP (Echo11, post process)

SWI mIP

(Echo12, FR) SWI

(Echo12, FR) Enhanced MRA Enhanced MRA MIP

(post process)

Original phase (Echo12, FR)

HP filtered phase (Echo12, FR)