spectrIm-QMRS 3.0.3 Alpha International

New in 3.0.3: the first official Linux release

spectrIm-QMRS 3.0.3 alpha international is now available for Windows 11 x64 and Linux x64. Both packages include their own Java and Python runtimes, NumPy and SciPy, and platform-specific ILV simulation and pthreads TDFDFit executables. Extract the complete package and use its startup script.

Still an alpha release. This version has been thoroughly tested in our workflows on Windows 11 and Ubuntu 22.04 under WSLg, but bugs may remain. Other Linux environments have not been verified to the same extent. Back up your data and models, check processing results carefully, and report problems with the relevant logs.

Major fixes and improvements

Siemens SVS-edit product sequence: spectrIm-QMRS can load and analyze edited single-voxel spectroscopy data, including three-instance Siemens XA60 acquisitions. Load an individual response or compute the difference between two user-selected instances, then continue with the standard SVS processing and analysis workflow.
Linux fitting and simulation: platform-aware executable paths and defaults allow the bundled native tools to run on Linux as well as Windows.
Prototype and summed-region fitting: corrected native-process invocation and result handling, with clearer reporting when a fit cannot complete.
Window placement: dialogs and secondary windows open centered over the relevant parent in the Clinical Viewer, TDFDFit modelling tools and ILV editors, while maximized windows remain maximized.
Online help stability: fixed the embedded browser lifecycle when closing and reopening help, addressing blank subsequent pages and application stalls observed during testing.

spectrIm-QMRS 3.0.3 showing a loaded Siemens SVS-edit dataset, the single-voxel location on a sagittal MR image, its spectrum, and three DICOM response instances; identifying text redacted — **Siemens SVS-edit: MEGA-type editing at TE = 68 ms.** A single-voxel dataset acquired on a Siemens 3 T scanner running XA60, loaded in spectrIm-QMRS 3.0.3 alpha international. The acquisition targeted 2-hydroxyglutarate (2HG) editing; this example was recorded in a healthy test volunteer and is not presented as evidence of 2HG detection. The Clinical Viewer shows the voxel location on the anatomical image, the resulting spectrum, and the three DICOM response instances. An individual response or the difference between two user-selected instances can be loaded for subsequent SVS processing and analysis. Identifying labels, dates, and file paths have been redacted.

Windows download and setup · Linux download and setup

Clinical Viewer GUI

New users can start with the main menu and toolbar overview. It explains how the Clinical Viewer is organized and links to the detailed v3 documentation pages for each menu.

spectrIm-QMRS Clinical Viewer showing an MRSI map overlay and selected spectra — Clinical Viewer in spectrIm-QMRS 3.0.2 Alpha International showing a SLOW-EPSI dataset displayed on top of the anatomical T1-weighted image stack acquired on a Terra 7T scanner, with MRSI map overlay, selected voxels, and linked spectrum display. spectrIm-QMRS v3.0.2 Alpha International supports Siemens legacy and enhanced XA-line DICOM spectroscopy data as well as Philips datasets.

International interface

The international interface lets users select the display language while keeping the same clinical MRS(I) workflow and tools. The example below shows the Clinical Viewer in Simplified Chinese.

spectrIm-QMRS 3.0.2 Alpha International Clinical Viewer displayed in Simplified Chinese with an MRSI map, spectrum, fitting progress, and quantification controls — spectrIm-QMRS 3.0.2 Alpha International displayed in Simplified Chinese, showing a 3D MRSI dataset, NAA map, spectrum, completed parallel TDFDFit processing, and quantification-map controls.

More features in the spectrIm-QMRS 3 series

Clinical Introduction to MRS(I)

A clinician-friendly overview of what MRS and MRSI measure, why quality control matters, and how processing connects spectra to metabolite maps. Start with the introduction.

No installation required

Distributed as self-contained Windows ZIP and Linux TAR.GZ packages including the required Java and Python runtime components.

International User Interface

The interface is available in English, Arabic, Chinese (Simplified), Czech, Danish, Dutch, Finnish, French, German, Hindi, Icelandic, Italian, Japanese, Norwegian Bokmål, Polish, Portuguese, Spanish, and Swedish. See the Chinese interface.

Advanced HLSVD Water Removal and Denoising

A more advanced HLSVD implementation provides fast residual water removal, denoising, and preprocessing of clinical MRS(I) datasets. See the interactive processing workflow.

3D CSI and MRSI Multiframe DICOM

Three-dimensional CSI and MRSI datasets can now be loaded from multiframe DICOM spectroscopy objects and displayed with their full spatial geometry.

Siemens Enhanced DICOM Support

Enhanced spectroscopy DICOM from Siemens XA software lines is accepted as valid input, while the legacy Siemens spectroscopy DICOM format remains supported.

Quantum-Mechanical Basis Set Simulator

Integrated ILV simulation solves the Liouville-von Neumann equations to generate quantum-mechanical metabolite basis spectra and multiplet-resolved components for prior-knowledge model construction. Open the simulator page.

SLOW-EPSI fitting support

SLOW FULL, PARTIAL, and DIFFERENCE datasets can be analysed with ILV-generated basis spectra, including shorter component names and resonance-group components for more flexible TDFDFit modelling. Open the SLOW-EPSI page.

Automatic TDFDFit Model Creator

Guided prior knowledge model creation to help clinicians start working with MRS(I) without requiring a spectroscopist as a direct colleague.

Two-Water-Compartment SVS Quantification

A two-water-compartment model supports LCModel-style absolute quantification of SVS data using a same-study water reference and compartment-corrected concentration estimates. Open the absolute quantification page.

Parallel POSIX-Threads TDFDFit

TDFDFit now performs prior-knowledge fitting in parallel with POSIX threads for faster processing across available CPU cores. Apply predefined models.

Summed-region TDFDFit

Clinicians can select a region of voxels, fit the summed spectrum as one higher-SNR spectrum with ΣQ!, and reopen named summed regions with Σ? to review the selected voxels, fitted overlay, and fitted parameters. Read the processing menu notes.

NIfTI / DICOM Conversion

A manual conversion window now supports scalar NIfTI-to-DICOM image-series creation and DICOM-to-NIfTI conversion through dcm2niix. Open the conversion page.

Clinical DICOM Workflow

A new crash course explains why DICOM receiving and DICOM formatted spectroscopy results matter in clinical MRS(I), and how this makes spectrIm-QMRS more than a standalone research processing tool. Read the crash course.

Secondary Capture DICOM Export

Clinical Viewer screenshots and selected local image files can be written as DICOM Secondary Capture objects using the last loaded spectroscopy DICOM examination as patient and study context. Open the workflow page.

United Imaging spectroscopy support in v3.1 alpha

From version 3.1 alpha onward, spectrIm-QMRS is planned to add support for United Imaging spectroscopy file formats alongside the existing DICOM-based Siemens and Philips example workflows.

Expert TDFDFit Modelling Frame

Prior-knowledge model construction for NMR/MR spectroscopy knowledgeable users: Voigt-line editing, prototype optimization, and parameter-linking documentation. Open the modelling frame page.

Manual MRUI Basis-Set Loading

Legacy expert route for loading externally simulated MRUI numeric basis patterns into TDFDFitControl. In v3 this route is complemented by the integrated ILV basis-set simulator. Open the walkthrough.

Clinical and research MRS(I) processing in one self-contained package