Application Guide & Release Notes Inner-volume-imaging (IVI) EPI C2P Release 002a 1 September 2015 TMII Translational and Molecular Imaging Institute
Conditions of Use This package is provided to support collaborative research projects between the Icahn School of Medicine at Mount Sinai (ISMMS) and University of Minnesota and users of Siemens MRI equipment, in accordance with a current C2P agreement. Authors Junqian Xu, Ph.D. Translational and Molecular Imaging Institute Icahn School of Medicine at Mount Sinai Edward J. Auerbach, Ph.D. Center for Magnetic Resonance Research University of Minnesota 1
Table of Contents Overview... 3 Sequence Description... 4 Hardware and Software Requirements... 5 Installation Procedure... 6 Usage... 7 Important Issues (not bugs)... 12 Known Bugs... 13 Version Changes... 14 Acknowledgment... 15 2
Overview Inner-volume-imaging (IVI) uses orthogonal excitation and refocusing RF pulses to selectively refocus the magnetization from a limited field of view (reduced FOV). In single shot spin echo EPI diffusion imaging, it has the advantage of reducing the EPI readout, hence reducing susceptibility related distortions, when imaging small anatomical structures, such as optic nerve, spinal cord, or prostate. To improve the signal-to-noise (SNR) efficiency, a pair of refocusing/inversion pulses can be applied in the phase-encoding direction in a driven equilibrium fashion. Experimental Combining multiband RF excitation with IVI has not been fully tested. More detailed information about the multiband pulse sequence and image reconstruction implementation can be found at the CMRR multiband C2P download page: www.cmrr.umn.edu/multiband 3
Sequence Description The pulse sequences in this package are based on the product ep2d_diff sequences from Siemens. More detailed information about the IVI EPI diffusion pulse sequence implementation can be found in the following references: 1. Jeong EK, Kim SE, Guo JY, Kholmovski EG, Parker DL. High-resolution DTI with 2D interleaved multislice reduced FOV single-shot diffusion-weighted EPI (2D ss-rfov-dwepi) Magn. Reson. Med., 54, 1575 1579, 2005 [PubMed] 2. Xu J, Shimony JS, Klawiter EC, Snyder AZ, Trinkaus K, Naismith RT, Benzinger TLS, Cross AH, Song SK. Improved in vivo diffusion tensor imaging of human cervical spinal cord. NeuroImage, 67, 64-76, 2013 [PubMed] The accompanying spinal cord DTI post-processing scripts can be downloaded from: http://sourceforge.net/projects/spinedti More detailed information about multiband pulse sequence can be found at the CMRR multiband C2P download page. 4
Hardware and Software Requirements Versions of the inner-volume-imaging EPI sequences will be available for three Siemens software versions, supporting several system types. It may be possible to use the sequences with other scanners not listed with below (e.g. 1.5T systems), but compatibility has not been tested. VB17A: MAGNETOM Trio (TQ-engine), MAGNETOM Verio 3T (VQengine), and MAGNETOM 7T. (Released) VD13A-SP4: MAGNETOM Skyra 3T (Skyra-XQ). (To be released) VD13D: MAGNETOM Prisma 3T. (To be released) 5
Installation Procedure Important: please install the CMRR Multiband C2P (development release) first! 1. Please skip this step unless errors are encountered in step 8: Restart the system (reboot host and MRIR, or restart image calculation and the syngo Exam task card). This is necessary to unload possibly locked shared objects. 2. Login as Advanced User. 3. Extract the.zip file to a temporary directory 4. Open a command window from Windows start menu -> run -> cmd. 5. Open ideacmdtool from the command window. 6. Choose 2 PAS unload, then type q to quit 7. Run the installer.bat file 8. If the installer reports any error, please restart the system and try again. 9. If a sample protocol is available for your system, it will appear at the end of the USER tree in the Exam Explorer. If a sample protocol is not available, create a default protocol in Exam Explorer by selecting Insert Sequence, USER, then tmii_ep2d_diff_ivi for the desired sequence variant. 6
Usage The sequence is based on the Siemens product ep2d_diff sequence; most of the protocol parameters are the same. The most important changes appear on the following measurement cards: Routine Card FoV phase: This parameter determines the IVI slab thickness in the phase encoding direction. The Phase oversampling parameter increases the slab thickness by the input percentage. Slice group: multiple slice groups are allowed for multi-slicemulti-angle (MSMA). (see Important Issues) Multi-band accel. factor: Ref. CMRR multiband C2P release note 7
Contrast/Common Card Magn. preparation: Slice-sel. IR and Non-sel. IR can be selective with monopolar diffusion scheme to provide double inversion for magnetization outside of the excited slice for efficient multi-slice imaging. The order of the IR and fatsat module is switched from the Siemens default to place IR after fatsat to minimize delays between the two refocusing/inversion pulses. Grad rev. fat suppr.: If enabled, the polarity of the slice select gradients will be reversed between the pair of refocusing/inversion pulses in the phase-encoding direction. This can provide effective fat suppression at no cost in time or SAR. However, it can also result in signal losses in areas of B0 inhomogeneity. 8
Physio/Signal1 Card Minimum TR is recommended to fit the protocol into the acquisition window. However, the actual TR = # slices * cardiac cycle * Trigger pulse. Acquisition window is typically chosen to be smaller than the average cardiac cycle. Trigger pulse is typically chosen to be one, unless the cardiac cycle is very fast (PP interval < 800 ms), in which case one may choose to skip every other pulse (Trigger pulse = 2) for SNR consideration. 9
Sequence/Part 1 Card Flow comp.: A flow compensated gradient wave form for the excitation slice selective gradient can be selected to reduce motion artifacts in b 0 image (spoilers in slice direction for refocusing pulse are also removed) and diffusion weighted images without b-vector in slice direction. Multi-slice mode: when physiological triggering is on, single-shot provides slice-by-slice triggering, while interleaved only triggers on the first slice. 10
Sequence/Special Card (Ref. CMRR multiband C2P release note) To enable experimental options, please create a text file C:\MedCom\MriCustomer\seq\MBAdvancedSettings.ini with the following contents: [MultiBand] RFPulseShape = 1 11
Important Issues (not bugs) This release will expire on 1 December 2014! Multi-slice-multi-angle (MSMA) is not compatible with Siemens DTI post-processing and mosaic functor. Disable Average ADC maps, Individual ADC maps, FA maps, Mosaic, and Tensor when MSMA is used. Only diffusion modes MDDW and Free are compatible with multi- band. The other modes have been disabled (diffusion vector in the PRS coordinates can be specified in the external DiffusionVectors file). The MDDW license is therefore required to insert the MB diffusion sequence. 12
Known Bugs When slice-selective IR or non-selective IR is selected with fat saturation (fatsat), the order of the IR and fatsat module is switched from the Siemens default to place IR after fatsat. However the displayed TI does not reflect this change. 13
Version Changes Release 002a, 1 September 2015 (jgx: vb17a/73410c6 multiband C2P R012b) Same as R002 with extended expiration date Release 002, 3 June 2014 (jgx: vb17a/d2af6b9 multiband C2P R011) UI: RF pulse shape and refocus pulse duration Release 001, 28 March 2014 (jgx: vb17a/37ca1d6 multiband C2P R010b) Initial public release 14
Acknowledgment Niels Oesingmann, Ph.D. Siemens collaboration manager Icahn School of Medicine at Mount Sinai product source code, MRA addendum, C2P management Agus Priatna, Ph.D. Siemens collaboration manager Washington University School of Medicine product source code, MRA addendum Funding Department of Defense (DOD):PC050667 National Multiple Sclerosis Society (NMSS): FG1782A1 initial IVI implementation NIH Human Connectome Project: U54MH091657-01 NIH NCRR: P41 RR008079 NIH NIBIB: P41 EB015894 multiband development Radiological Society of North America (RSNA): RSCH1328 TMII and Department of Radiology: Icahn School of Medicine Capital Campaign integration of multiband with IVI/rFOV techniques 15