Map Menu

Map menu, version 3.0.1 Alpha

Current version 3.0.1 Alpha Map menu screenshot.

Clear Map

Removes the current color map overlay from the viewer. This does not delete spectroscopy data, fitted results, or imported files; it only clears the currently displayed map state.

Map Features

Opens the feature-map interface. This interface lets the user create maps from built-in spectral features. The current source includes feature functions such as FD peak SNR, FD magnitude sum, FD absorption sum, FD region ratios, phase, TD and FD noise, TD and FD mean, standard deviation, skewness, kurtosis, TD mean SNR, quality map, temperature, and TDFDFit quality number.

Some features require one or two user-defined spectral ranges. For example, a frequency-domain ratio map needs two frequency ranges, while SNR-like maps need a signal or noise interval. These ranges are selected in the map-feature dialog and should be checked against the acquisition and nucleus being reviewed.

Map Quantification Results

Creates maps from available quantification results. For legacy workflows this can use jMRUI-style quantification results. When TDFDFit results are available, spectrIm-QMRS opens the TDFDFit results map interface using the available metabolites and feature names from the TDFDFit result store.

This command is central after fitting: it turns fitted amplitudes, frequency shifts, damping parameters, quality numbers, or other fitted features into spatial maps for review and reporting.

The current version 3.0.1 Alpha dialog also includes interactive auto-scale clipping, so outlier voxels can be handled without changing the underlying fitted values. The dedicated guide describes how to launch the dialog, choose fitted quantities, clip outliers, mask excluded voxels, and apply Gaussian smoothing to the displayed map.

Open Map Quantification Results guide

Print Map Statistical Parameters (All Voxels)

Prints statistical parameters for the current map using all voxels. The old website described this as a way to compute statistical values for the intersection between the spectroscopy volume and the background image. In the current v3 menu this item operates on the displayed map values.

Typical values include the number of voxels or pixels, minimum, maximum, mean, standard deviation, skewness, and kurtosis.

To be checked manually: confirm the exact printed fields for version 3.0.1 Alpha and whether image-pixel statistics are still included or only voxel map values are reported.

Print Map Statistical Parameters (Selected Voxels)

Prints statistical parameters only for the currently selected voxels. This is useful when a lesion, reference region, contralateral region, or manually selected ROI should be summarized separately from the rest of the grid.

The selected-voxel variant is particularly useful after MRSI voxel selection, because the same selected region can be used for fitting, reporting, and map statistics.

Create Map from .MAT

Creates a map from a MATLAB .mat file. This allows externally computed voxel-wise values to be brought back into spectrIm-QMRS for visual inspection on the anatomical image and MRSI grid.

To be checked manually: document the required variable names, matrix dimensions, and voxel ordering expected by the importer.

Export Map values to .MAT

Saves the current map values to a MATLAB .mat file. If the selected filename does not end in .mat, the application appends the extension automatically.

Export Normalized Map values to .MAT

Saves a normalized version of the current map values to a MATLAB .mat file. This is intended for workflows where absolute map values are less important than a normalized spatial pattern or when maps must be compared across datasets.

To be checked manually: describe the normalization formula used by saveMapToMAT(..., true).

Correct Map from .MAT file

Applies a correction template from a MATLAB .mat file to the current map and updates the image panels. This can support correction workflows where an externally generated template or selection profile is used to adjust map values.

To be checked manually: document the required template format and intended correction use case.

Import external label .CSV file

Imports externally prepared label or overlay data from a CSV file. The Java code loads the CSV overlay label file and opens an overlay-selection frame where the user can choose how the imported columns should be interpreted and displayed.

This is useful when external segmentations, clinical labels, research annotations, or non-spectroscopic measurements need to be viewed in spatial relation to the MRSI grid.

To be checked manually: document the CSV header conventions, accepted column data types, and how imported labels are matched to voxels or image locations.

Older Map page content

The previous website page mentioned auto-windowing, background MRI color scales, and image segmentation within selected spectroscopic regions. These functions are not visible in the current version 3.0.1 Alpha Map menu screenshot.

To be checked manually: determine whether these functions moved to another menu, were removed, or should become a separate advanced image-overlay page.

Legacy assets

The old Map help page referenced the common spectrIm and EU project logos but did not include menu-specific screenshots. The referenced legacy images have been copied into assets/img/legacy/map for traceability.