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MIDAS eNewsletter

 

MARCH, 2022

News

This newsletter marks a transition in the MIDAS project. After 20 years of NIH funding the project will finish in April 2022. There are no plans to apply for new funding to continue the development effort; however, this does not mean an end to the project!  The web site will continue to remain active; we will continue providing releases for newer versions of IDL and the Siemens IDEA software; and we will still be available to answer questions. The main difference will be that we will no longer be able to provide custom support for users of the MIDAS software and we do not anticipate any major new developments.

There are, however, plans for new development efforts for both the MIDAS and EPSI products under new funding and new investigators, and new efforts are already taking place under collaborative projects, some of which are described below. 

Developing Projects

Multiple sites make use of the EPSI/MIDAS developments and we are pleased to have been part of many important research publications (see below for the lates), but here we would like to highlight just a few of the projects that will be continuing with new developments that will expand on the capabilities initially developed under the MIDAS project:

1. Spectroscopic MRI-guided Radiation Dose Escalation for Newly-Diagnosed Glioblastoma.

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Description automatically generatedDrs. Shim and Shu (Emory University) have recently published results of a three-site clinical trial that provide compelling evidence for the value of volumetric MRSI to delineate brain regions for an escalated radiation dose for treatment of GBM (Ramesh et al. Neuro-Oncology Advances, vdac006, In Press 2022). Based on a study of 30 subjects with a median follow-up of 21.4 months, the median overall survival was 23.0 months, which compares favorably to that of standard treatment (16.3 months). A funding request to extend this clinical trial has been well received and the project will be continued in late 2022. This multisite project will ensure that the EPSI sequence will continue to be maintained on the newer versions of the Siemens MRI scanners for several more years.

An example result from the study of Shim et al. is shown in the figure on the right, which illustrates the method for segmentation of a GBM based on the volumetric MRSI result, using NAA/Cho>2.0, which was used as a target for escalated dose radiation treatment. The display and segmentation use a custom-built web-based software platform, the Brain Imaging Collaboration Suite (BrICS), developed by Dr. Shim’s group, that reads the data produced by the MIDAS reconstruction. Additional software developments are being carried out to simplify the metabolite image reconstruction.

2. Spectral editing MRSI at 7T.

Drs. Slotboom and Weng (University of Bern), with support from Sulaiman Sheriff at Miami, have modified the EPSI sequence to (a) work at 7T, and (b) to include a chemical-selective adiabatic 2p-pulse pair for spectral editing. The sequence is robust to B1 inhomogeneities and has been demonstrated to provide excellent spectral quality for full (i.e. non-edited) spectra and for spectrally-edited mapping of GABA and phosphoethanolamine. The paper is currently In Press (Magn. Reason. Med. 2022).

The figure to the right shows an example of non-edited spectra obtained at 7T, from a patient with a brain tumor. This data was obtained with TE = 82 ms, TR = 1551 ms, matrix size = 65 × 28 × 14 (4.3 × 7.9 × 7.9 mm), and a measurement time = 7:41 min.

3. Higher Resolution EPSI.

In collaboration with Drs. Barker and Ouwerkerk (Johns Hopkins University) we have implemented the EPSI sequence with a dual-band hypergometric RF pulses for water and lipid suppression. This replaces the inversion-nulling method for lipid suppression, thereby providing increased sensitivity, which enables improved spatial resolution. The figure to the right shows an example result for a normal subject. This was obtained using a nominal spatial resolution of 4x4x6 mm3 and acquired in 10.5 minutes.

The reliability of the modified sequence remains a concern, with B0 inhomogeneity and motion affecting lipid contamination, and further optimization of the method continues.

3. EPSI for GE.

The original project for the EPSI development also included versions of the sequence for GE and Philips scanners. These were no longer maintained after then end of that project, but over the years there has continued to be interest in running the volumetric EPSI on these other scanners. Dr. Brian Soher (Duke University) is currently updating the GE sequence code to work with the latest versions of their scanners.

 

Software - New and Improved

 

FITT: : An option has been added to decrease the time to obtain the initial parameter estimates by subsampling the voxels tested. This “Subsample factor” is located in the “Initial” tab, as shown here:

 A subsampling value of three provides a factor of almost nine decrease in time for the initial values estimate, with no impact on the final result. For our “standard” resolution EPSI protocol (e.g. 50x50x18 points) this change only provides a saving of a few minutes, but this can provide a significant reduction in processing time for higher resolution images, which are currently under development.

The MIDAS Toolbar: A couple of changes have been made to the toolbar:

1) The icons for FITT2 and MRISEG have been removed as these have been superseded by FITT2.1  and IDLSEG . However, the previous versions of these programs are still included in the distribution and can be called from the BATCH pipeline if needed for backward compatibility.

2) The link to the MIDAS Documentation (from the  icon) now goes to the documents page on the web site, and not the local files that are included in the distribution. This helps us maintain the latest versions of these files.

Support for Siemens IDEA version XA: We are currently working on supporting the EPSI pulse sequence under software versions XA20 and XA30.

 

MIDAS Tips, Questions, and Answers

 

EPSI and Processing Pipeline Versions: Over the roughly 20 years that the MIDAS processing pipeline has been developed we have gone through several versions of the scanner software and the EPSI sequence, and we have developed different versions of the batch processing pipelines to exploit new features, for example to add PCA denoising or temperature mapping. There are also different files for studies using phantom objects or computers with large RAM that can speed up the GRAPPA reconstruction. When program changes have been made that added new processing parameters the old processing files still maintained backward compatibility, though the programs may prompt the user to re-save the processing file so that the new options are added.

Throughout this time, we have always maintained a “standard” processing pipeline for the most current version of the Siemens/IDEA software version on the web site, though with the evolving nature of these pipelines we have not kept track of the many variants. We always advise that once a project has started the processing remain unchanged throughout. However, it is also worth remining you that it is possible to update the MIDAS software version and the processing files, and to then reprocess all studies using the BATCH program, ensuring consistency.

The latest versions of the “standard” pipeline are in the Processing Files section of the MIDAS Downloads page of the web site, in the file ProcFiles_3T_ShortTE_SkyraPrisma_WIP.zip. This file also includes a summary of the different pipelines in “readme_batch_processing_files.txt”.

 

Developer’s Corner

 

MIDAS Toolbar Utilities: The MIDAS toolbar includes a “Misc. Tools” icon , which brings up a list of utility functions (shown on the right). Historically, these are utilities that have been developed to help with specific projects and may not be of interest to most users. However, the user can change this list to make it more useful to them, by editing the file:

*:\midas\bin\utilities\MIDASTools_Misc_Tools_List.txt

(where *: is the drive/directory used for your MIDAS distribution).

This file contains a simple comma separated list that defines the IDL procedure to run and a description of that program, i.e.

makesidata, SI Simulation.

In this case, the procedure @runmakesidata is run from the IDL command line and the test “SI Simulation” appears in the widget display.

It is also possible to use this feature to run programs from the Windows command line, for example, to run the browser Chrome, you would first create a file with the SPAWN command for this program, e.g.:

   PRO RUNCHROME

      spawn, '"C:\Program Files\Google\Chrome\Application\chrome.exe"', /nowait

   END

In this command the ".." is required by Windows because of the space in “Program Files”, and the '..' defines the string in IDL. Now add that command to the list in the MIDASTools_Misc_Tools_List.txt file:

runchrome, Google Chrome

For this example, the RUNCHROME procedure would be compiled at run time, for which the run-time license is required, therefore, this cannot be done under the virtual license.  To run under the VM license a save file must be created and the MIDAStools program would restore this before running the command. Other examples of programs that we have found useful and could be added to the utilities option are MRICro, for display of Analyze format images, and Notepad++, for viewing and editing the XML files.

 

Publications

 

Many thanks to our collaborators for these recent reports (since 2018):

·        Ramesh K, Mellon EA, Gurbani SS, Weinberg BD, Schreibmann E, Sheriff SA, Goryawala M, de le Fuente M, Eaton BR, Zhong J et al. A Multi-Institutional Pilot Clinical Trial of Spectroscopic MRI-guided Radiation Dose Escalation for Newly-Diagnosed Glioblastoma. Neuro-Oncology Advances, vdac006, In Press, Published: 27 January 2022.

·        Weng G, Radojewski P, Sheriff S, Kiefer C, Schucht P, Wiest R, Maudsley AA, and Slotboom J. SLOW: A novel spectral editing method for whole-brain MRSI at ultra high magnetic field. Magn. Reason. Med. 2022. doi: 10.1002/mrm.29220

·        Ahlswede M, Nösel P, Maudsley AA, Sheriff S, Mahmoudi N, Bronzlik P, Lanfermann H, Ding X-Q. Alterations of Striato-Thalamic Metabolism in Normal Aging Human Brain -An MR Metabolic Imaging Study. Metabolites. 2021; 11(6):371.

·        Lin JC, Mueller C, Campbell KA, Thannickal HH, Daredia AF, Sheriff S, Maudsley AA, Brunner RC, Younger JW. Investigating whole-brain metabolite abnormalities in the chronic stages of moderate or severe traumatic brain injury. PM&R. 2021 Apr 30.

·        Bustillo JR, Mayer EG, Upston J, Jones TR, Garcia C, Sheriff S, Maudsley AA, Tohen M, Gasparovic C, Lenroot R. Increased glutamate plus glutamine in the right middle cingulate in first episode schizophrenia but not in bipolar psychosis: A whole brain 1H-MRS study. Frontiers Psychiatry, 2021 Jun 7;12:660850

·        Sung, D., Kottke, P.A., Risk, B.B. et al. Personalized predictions and non-invasive imaging of human brain temperature. Commun Phys 4, 68 (2021).

·        Sharma AA, Nenert R, Mueller C, Maudsley AA, Younger JW, Szaflarski JP. Repeatability and Reproducibility of in-vivo Brain Temperature Measurements. Front Hum Neurosci. 2020 Dec 23;14:598435.

·        Bartnik-Olson BL, Alger JR, Babikian T, Harris AD, Holshouser B, Kirov II, Maudsley AA, Thompson PM, Dennis EL, Tate DF, Wilde EA, Lin A. The clinical utility of proton magnetic resonance spectroscopy in traumatic brain injury: recommendations from the ENIGMA MRS working group. Brain Imaging Behav. 2021 Apr;15(2):504-525.

·        Bustillo JR, Upston J, Mayer G, Jones T, Maudsley AA, Gasparovic C, Tohen M, Lenroot R. Glutamatergic hypo-function in the left superior and middle temporal gyri in early schizophrenia: a data-driven three-dimensional proton spectroscopic imaging study. Neuropsychopharmacology. 2020 Oct;45(11):1851-1859

·        Maudsley AA, Andronesi OC, Barker PB, Bizzi A, Bogner W, Henning A, Nelson SJ, Posse S, Shungu DC, Soher BJ. Advanced magnetic resonance spectroscopic neuroimaging: Experts' consensus recommendations. NMR Biomed. 2020 Apr 29: e4309.

·        Goryawala M, Sullivan M, Maudsley AA. Effects of apodization smoothing and denoising on spectral fitting. Magn Reson Imaging. 2020 Jul;70:108-114.

·        Kahl KG, Atalay S, Maudsley AA, Sheriff S, Cummings A, Frieling H, Schmitz B, Lanfermann H, Ding XQ. Altered neurometabolism in major depressive disorder: A whole brain (1)H-magnetic resonance spectroscopic imaging study at 3T. Prog Neuropsychopharmacol Biol Psychiatry. 2020 Jul 13;101:109916.

·        Goryawala M, Saraf-Lavi E, Nagornaya N, Heros D, Komotar R, Maudsley AA. The association between whole-brain MR spectroscopy and IDH mutation status in gliomas. J Neuroimaging. 2020 Jan;30(1):58-64.

·        Chiappelli J, Rowland LM, Wijtenburg SA, et al. Cardiovascular risks impact human brain N-acetylaspartate in regionally specific patterns. Proc Natl Acad Sci U S A. 2019; 116: 25243–25249.

·        Maghsudi H, Schütze M, Maudsley AA, Dadak M, Lanfermann H, Ding XQ. Age-related Brain Metabolic Changes up to Seventh Decade in Healthy Humans: Whole-brain Magnetic Resonance Spectroscopic Imaging Study. Clin Neuroradiol. 2020 30(3):581-589.

·        Klietz M, Bronzlik P, Nösel P, Wegner F, Dressler DW, Dadak M, Maudsley AA, Sheriff S, Lanfermann H, Ding X-Q. Altered neurometabolic profile in early Parkinson’s disease: a study with short echo-time whole brain MR spectroscopic imaging. Frontiers Neurol. 2019 Jul 17;10:777.

·        Verma G, Chawla S, Mohan S, Wang S, Nasrallah M, Sheriff S, Desai A, Brem S, O'Rourke DM, Wolf RL, Maudsley AA, Poptani H. Three-dimensional echo planar spectroscopic imaging for differentiation of true progression from pseudoprogression in patients with glioblastoma. NMR Biomed. 2019 32(2):e4042.

·        Gurbani SS, Sheriff S, Maudsley AA, Shim H, Cooper LAD. Incorporation of a spectral model in a convolutional neural network for accelerated spectral fitting. Magn Reson Med. (2019) 81(5):3346-3357.

·        Maghsudi H, Schmitz B, Maudsley AA, Sheriff S, Bronzlik P, Schütze M, Lanfermann H, Ding X. Regional metabolite concentrations in aging human brain: comparison of short-TE whole brain MR spectroscopic imaging and single voxel spectroscopy at 3T. Clin Neuroradiol. 2020 Jun;30(2):251-261.

·        Mueller C, Lin JC, Sheriff S, Maudsley AA, Younger JW. Evidence of widespread metabolite abnormalities in Myalgic encephalomyelitis/chronic fatigue syndrome: assessment with whole-brain magnetic resonance spectroscopy. Brain Imaging Behav. 14(2):562-572 (2020)

·        Gurbani SS, Schreibmann E, Maudsley AA, Cordova JS, Soher BJ, Poptani H, Verma G, Barker PB, Shim H, Cooper LAD. A convolutional neural network to filter artifacts in spectroscopic MRI. Magn. Reson. Med. 80(5):1765-1775 (2018).

·        Maudsley AA. Lesion segmentation for MR spectroscopic imaging using the convolution difference method. Magn Reson Med. 81(3):1499-1510 (2019)

·        Goryawala MZ, Heros DO, Komotar RJ, Sheriff S, Saraf-Lavi E, Maudsley AA. Value of diffusion kurtosis imaging in assessing low-grade gliomas. J Magn Reson Imaging. (2018) Mar 23. doi: 10.1002/jmri.26012.

·        Zhang Y, Taub E, Salibi N, Uswatte G, Maudsley AA, Sheriff S, Womble B, Mark VW and Knight DC. Comparison of reproducibility of single voxel spectroscopy and whole-brain magnetic resonance spectroscopy imaging at 3T. NMR Biomed. 31(4):e3898. (2018).

·        Goryawala MZ, Sheriff S, Stoyanova R, Maudsley AA. Spectral decomposition for resolving partial volume effects in MRSI. Magn Reson Med. 79(6):2886-2895 (2018).

·        J. Mauler, A.A. Maudsley, K-J. Langen, O. Nikoubashman, G. Stoffels, S. Sheriff, P. Lohmann, C. Filss, N. Galldiks, E. Rota Kops, N.J. Shah. Spatial Relationship of Glioma Volume Derived from FET PET and Volumetric MRSI: a hybrid PET-MRI study. J. Nuc. Med. 59(4):603-609 (2018).

·        Ding X-Q, Maudsley AA, Schweiger U, Lichtinghagen R, Bleich S, Lanfermann H, Kahl KG. Effects of a 72 hours fasting on brain metabolism in healthy women studied in vivo with magnetic resonance spectroscopic imaging. J Cereb. Blood Flow Metab. 38(3):469-478 (2018).

 

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