File
Loading, mounting, importing, exporting, DICOM header inspection, NIfTI/DICOM image conversion, settings, and unloading of image or spectroscopy data.
Clinical Viewer GUI
Main Menu and Toolbar
The main menu is the entry point to the spectrIm-QMRS Clinical Viewer. It connects DICOM loading, image display, MRSI voxel selection, preprocessing, TDFDFit quantification, map generation, reports, quality control, DICOM networking, and clinical case navigation.
GUI orientation
The Clinical Viewer is organized around one central working surface: anatomical images and spectroscopy voxel overlays are shown on the left, spectra are shown on the right, processing and fitting controls sit below the spectrum viewer, and the lower part of the window contains the mounted Patient/Study Browser and the DICOM instances belonging to the selected series.
The toolbar gives fast access to frequently used commands such as mounting DICOM directories, refreshing model selections, launching TDFDFit-related actions, HLSVD processing, apodization, offset and phase correction, and selected model operations. The exact enabled state depends on the loaded dataset and current selection.
Main menu and toolbar
The screenshot below shows the current version 3.0.1 Alpha main menu and toolbar. The toolbar has been updated together with the v3 GUI and gives direct access to frequently used loading, preprocessing, modelling, HLSVD, offset/phase correction, TDFDFit, and model-selection actions.
Top-level menus
View
Visibility settings for patient information, slice orientation, MRSI grids, overlays, color bars, original/fitted spectra, and spectrum differences.
Image
Image windowing, color tables, anatomical image statistics in selected spectroscopy regions, and WM/GM/CSF segmentation support.
MRSI Voxel Selection
Selection of all, excited, inner, feature-filtered, freehand, mirrored, preset, and tumor-region voxel groups.
Processing
Preprocessing, HLSVD water removal, denoising, offset and phase correction, TDFDFit model creation, fitting, result handling, and batch processing.
Map
Display, correction, import/export, and statistical reporting of fitted or derived spectroscopy maps.
Reports
Standard and custom report creation for quantification results, including templates for repeatable clinical or research output.
Quality Control
Manual and consensus spectral labelling, label analysis, and custom spectral-quality classifier support.
jMRUI Import/Export
Legacy exchange functions for jMRUI spectra and results. This connection is now largely superseded by internal TDFDFit functionality and is planned for removal in version 3.1.
DICOM Network
DICOM node configuration, listener and renaming control, and automatic-processing concepts for clinical network workflows.
Clinical Cases
Patient-browser functionality for clinical navigation and analysis of MRS(I) results stored in the patient database.
Help
About information, contributor acknowledgement, and online help access.
Clinical and expert paths
Clinical users should normally start with the guided workflow: load or mount DICOM data, inspect spectra in anatomical context, use automatic model creation where possible, and apply predefined TDFDFit models using the parallel CPU fitting engine.
Spectroscopy experts can go deeper into manual prior-knowledge modelling, basis-set simulation, and detailed fitting strategy definition. These expert pages are linked below because they are central to version 3.0.1 Alpha.