Spectrum Estimation Solver

One of the fundamental blocks of DRSuite is the spectrum estimation. This takes 2D/3D spatial data acquired at multiple encodings in DRsuite compatible format and calculates its voxelwise spectrum. The user must ensure that the volumes are properly registered before proceeding.

• If the data is 2D, the tool calculates voxelwise spectra for the 2D slice at once.

• If the data is 3D, the tool calculates voxelwise spectra for each 2D slice separately.

This tool can be run from the command line via the script with the required name value pairs:

SH

spectEstimation.sh -imgfile  imgfile_name -spect_infofile spect_infofile_name -configfile configfile_name -outprefix outprefix_name

MATLAB

spectEstimation('imgfile','____', 'spect_infofile', '____','configfile','____','outprefix','____',)

Or with additional optional name value pairs:

SH

spectEstimation.sh -imgfile  imgfile_name -spect_infofile spect_infofile_name -configfile configfile_name -spatmaskfile spatmaskfile_name -outprefix outprefix_name

MATLAB

spectEstimation('imgfile','____', 'spect_infofile', '____','configfile','____','spatmaskfile','____','outprefix','____',)

Required Inputs

• imgfile:

  Filename of the .mat file storing the MR data related information. Details of the file format can be found here. The user must create this file before proceeding with spectrum estimation.

• spect_infofile:

  Filename of the .mat file containing spectrum-related information. The user needs to create this file based on user selected spectral points and should follow the fileformat mentioned here. This tool can handle multiple spectral dimension (including 1D spectra) as long as this file is stored in the given format.

• configfile:

  Filename of the .ini file storing spectrum estimation algorithm parameters. The spectrum estimation can be done using three algorithms -LADMM, ADMM, NNLS. The file format is described here.

• outprefix:

  a string input for the filename where the output of the spectrum estimation tool will be stored.

Optional Inputs

• spatmaskfile:

  Filename of the .mat file storing the binary spatial mask for the MR input data. This specifies voxel locations where spectrum estimation should be done. The spatial dimension of the variable in this file must match with the spatial dimension of the input data. This input field is optional to the spectrum estimation tool and when this input is not provided, spectEstimation.sh estimates spectra for the whole input volume. See here for file format.

Output

The software writes a single file into the folder specified in outprefix. This output file contains multiple fields which are described in detail here. This resulted output file is then used by visualisation tools to dive deep into the microstructural information.

Citation

If you use ADMM algorithm for your spectral estimation, please cite:

Kim et al., Diffusion-relaxation correlation spectroscopic imaging: A multidimensional approach for probing microstructure, 2017. DOI: 10.1002/mrm.26629

Liu et al., An Efficient Algorithm for Spatial-Spectral Partial Volume Compartment Mapping With Applications to Multicomponent Diffusion and Relaxation MRI,2025. DOI: 10.1109/TCI.2025.3609974

If you use LADMM algorithm for your spectral estimation, please cite:

Liu et al., An Efficient Algorithm for Spatial-Spectral Partial Volume Compartment Mapping With Applications to Multicomponent Diffusion and Relaxation MRI,2025. DOI: 10.1109/TCI.2025.3609974