FAQ - The EPSI sequence and MIDAS software

What is EPSI and MIDAS?

MIDAS provides data processing and analysis functions for MRSI data. It can support several MRSI acquisition variants, however, it is optimized for the volumetric proton EPSI acquisition and these two packages are generally distributed together.

Is EPSI+MIDAS useful for my application?

The volumetric EPSI acquisition aims to sample a large fraction of the brain with relatively good spatial resolution and the MIDAS processing is optimized for this type of data. It samples a much larger brain volume than vendor-provided implementations of SI; however, there are some trade-offs to this approach which means it may not be the best for all applications.
While MIDAS has many novel features for processing SI data, it is not anticipated that it would provide improved quality over the vendor-provided reconstruction for the standard 2D SI acquisitions. There can also be some restrictions on getting the raw k-space data off the scanner for the vendor-provided sequences that limit what can be done.
For more specialized MRS applications, e.g. 7T, spectral editing, or different k-space schemes, it is likely that additional code development by the recipient would be needed, but we would be pleased to help with that.

Can EPSI/MIDAS be used for clinical studies?

Only with appropriate institutional approvals. These are provided for investigational studies only.

How do I get the EPSI sequence?

This sequence is available for 3T instruments from GE, Philips, and Siemens, and procedures differ for each:

  • Siemens: For VD13A/D and VE11A/B/C software versions (Skyra and Prisma) the EPSI sequence is distributed as WIP 814. Contact your local Siemens collaboration scientist for distribution. For software version VB (Trio) the sequence is distributed as a C2P, which requires that the user obtains a letter from Siemens authorizing distribution of the EPSI sequence from the University of Miami. For the C2P/VB distribution only there is also a requirement to complete a materials transfer agreement with the University of Miami, which can be downloaded from the link below. Not all software variants are supported and in some cases a simple recompilation at your site may be needed following a request for the source code.
  • GE: The sequence has been implemented on the MR750 and Signa platforms. Please contact Dr. Dan Spielman, University of Stanford for additional information.
  • Philips: The sequence has been implemented on the Achieva platform. Please contact Dr. Peter Barker, Johns Hopkins University.

What is included in the latest version of the EPSI sequence?

  • The EPSI sequence for VE11C includes real-time frequency adjustment and spatial reconstruction on the scanner. The on-line reconstruction removes the problem of dealing with the large raw data sizes; however, there remain some limitations depending on the available scanner memory and data sizes. Contact the developers for more details. Spectral reconstruction and fitting is still done off-line and the corresponding MIDAS processing pipeline is required for this.

This implementation of EPSI samples the whole brain. Isn't this a problem for MRS?

  • The standard setup uses automatic shimming, as for any MRI sequence, although there can be a benefit to using some additional manual shimming adjustment.
  • The sampled volume includes a large fraction of the brain, including the cortical surface, but there will always be regions where MRS data cannot be obtained. Depending on the scanner, between 60 to 70% of the brain can generally be sampled.
  • There are several trade-offs to the volumetric SI approach, however, the method has been found to have a reliability and data quality equivalent to or better than other SI implementations. The methods used to sample a large fraction of the brain involve a trade-off with sensitivity so, for example, it may not be the best method for imaging glutamate in central white matter. The use of reduced phase encoding and the long acquisition time (10 to 20 minutes depending on resolution) also increases sensitivity to subject motion.

How do I get the MIDAS software?

MIDAS is available to academic research sites at no cost and is distributed under the GNU General Public License. To obtain the software you must read our license agreement and send an email to the MIDAS team (amaudsley at Miami dot edu) that includes a statement that you agree with the terms of the agreement and are requesting a login. You must provide an institutional email address. An account will then be created for you that enables access to the download page. It would also be useful if you could tell us which MR instrument you will be acquiring data on.
The package is provided in a self-extracting zip file that installs easily on Windows PCs. Development is ongoing and it is recommended that you update your installation regularly to get the latest version. Also available for download are example processing files and sample data used in the tutorials.

What is needed to run MIDAS?

MIDAS requires IDL running under Windows OS on 64-bit CPUs. It can also be run under Linux using a Virtual Machine with Windows OS. IDL can be purchased from Harris Geospatial Solutions. Prices for academic licenses start at ~$300 for a node-locked license and $480 for a floating license (July 2016). There is also a run-time RT license that offers a lower cost for non-academic sites.
It is also possible to use the free IDL Virtual (VM) license, but there are two limitations: 1) multicore processing is not supported. The speed improvement with a full IDL license on a multi-core CPU is substantial for the spectral fitting. 2) The IDL log window is not shown (also the case with the RT license), meaning that informational messages and the occasional unhandled error messages cannot be seen. You can download the Virtual Machine version from Harris. This is free but requires that you set up an account with them.
With the full IDL license the spectral fitting will go much faster with multi-core CPUs, but there is not much benefit to having more than 12 cores. A minimum of 6Gb RAM is recommended, and up to ~16Gb for multi-core systems. A high resolution display is essential and a large monitor is highly recommended. A high speed disk I/O has also been found to be useful to handle the large datasets.

Can I add my processing/display/analysis module to MIDAS?

Absolutely! The processing pipeline is highly configurable and can run IDL procedures or any other program from a command line call. The parameter information is maintained using a XML format so some software development may be needed, but examples are available to access this using Java, Python, or IDL.

Can I get the source code?

Yes, all IDL and Java source code is provided as a separate download from the web site to registered users. The code is being actively developed, so before making changes to any code it is recommended that you contact the developers to be sure you have the latest version. Direct access to the source-code control system can also be provided to major developers. As per the license agreement, modifications to the source code should be submitted to inclusion in the distribution.

What are some of the limitations of MIDAS?

  • This is a large package that requires time and effort to fully understand. However, if you stay with the standard methods, for which an automated processing pipeline is available to download, then most users are up and running quickly.
  • The MRSI reconstruction is done off-line from the scanner. If the spatial reconstruction is not done on the scanner then the raw SI data has to be transferred to a local computer for processing. These are large datasets, e.g. 42 Gb for 32-channel detection.
  • For multi-channel acquisitions the data processing can take up to two hours, and longer if you run the VM version of IDL.
  • Integration with PACS systems is not included in the standard distribution, but can be provided using a module that requires the IDL DICOM license. Contact the MIDAS team for details. It is also possible to export metabolite images in DICOM format.
  • Our ability to provide custom support for individual users is limited; however, we are pleased to answer questions, to discuss ideas for developing new features, and to develop collaborative projects. Site visits and instruction can also be arranged.

How do I get started using MIDAS?

  • Extensive documentation is available with the distribution (look under Documents subdirectory) and on this web site.
  • Start with the tutorial, which uses a small 2D SI dataset that can be downloaded from the web site. When you have gone through that there is another example using a volumetric SI dataset that can be downloaded from the FTP site. Contact the MIDAS team for the FTP login information.
  • You should start with the automated processing pipelines that are provided on the web site, but as you gain experience you may then want to modify these processing steps to suit your protocols.
  • Instruction can be arranged. An informal course is available that takes roughly two-days. This is outlined in this document .

How do I cite MIDAS?

There are two main reports that describe the MIDAS software:

  • AA Maudsley, C Domenig, V Govindaraju, A Darkazanli, C Studholme, K Arheart, and C Bloomer. Mapping of brain metabolite distributions by volumetric proton MRSI. Magn. Reson. Med. 61: 548-559 (2009).
  • M Sabati, S Sheriff, M Gu, J Wei, H Zhu, PB Barker, DM Spielman, JR Alger, AA Maudsley. Multi-Vendor Implementation and Comparison of Volumetric Whole-Brain Echo-Planar MR Spectroscopic Imaging. Magn. Reson. Med., 74(5):1209-20 (2014).

Can I get some existing MRSI data?

Yes, all data taken at this site is made available. We have over 190 normal control datasets for TE=70 ms and additional data is being acquired for TE=17 ms. Studies from several clinical projects can also be made available, including TBI, brain cancer, and epilepsy. If you want to have access to the patient studies or to do more than just take a quick look at an example dataset a data use agreement is available.

EPSI Software Agreement

The following agreement is only needed for the older Siemens VB17 version of the EPSI sequence, which is distributed as a "P2P". This must be signed by an authorized institutional official (not the researcher). The signed agreements can be scanned and emailed, but if your institution requires originals then 3 copies are required.

  • EPSI Sequence MTA. Note: This is NOT needed for the Siemens Prisma & Skyra versions. Contact you local Siemens support to get the WIP for those.

Please send the signed agreement to the U. Miami Technology Transfer Office at email address um.ott.mta@…