Overview

This tab allows you to perform macromolecule removal. During an interleaved acquisition, both a full spectrum containing all metabolites and macromolecules, as well as a macromolecule spectrum are acquired. The macromolecule spectrum must be subtracted from the full spectrum prior to quantification of metabolite signals.

Load in the .dat Files

To perform macromolecule removal, you must first load in the *.dat files for the full spectrum and the macromolecule spectrum. Ensure any residual water signal has been removed from these spectra. Use the first two panels to load in these files. For each file, hit the Browse button to select the file, and hit the Confirm button to load the file.

Once the files are loaded, they will be plotted in the right panel.

Set the HSVD Parameters

The next step is to specify the Hankel singular value decomposition (HSVD) parameters. APPS uses HSVD to model the macromolecule signal to produce a noiseless version of the macromolecule spectrum. This noiseless version of the macromolecule spectrum is subtracted from the full spectrum to produce the metabolite only spectrum.

The parameters of the HSVD that you can adjust are as follows:

• Number of Points: The number of initial points along the FID to use in forming the Hankel Matrix
• Hankel Matrix Row/Col Ratio: The ratio of the number of rows to the number of columns of the Hankel Matrix
• Signal Related Singular Values: The number of Lorentzian peaks in the model

Run the Macromolecule Removal

Hit the Run Macromolecule Removal button to perform the macromolecule removal. The removal is performed as follows:

where is the macromolecule removed (metabolite only) signal, is the metabolite + macromolecule (full) signal, is the HSVD model of the macromolecule signal, is the scaling factor for the full signal, and is the scaling factor fo the macromolecule signal.

After running the macromolecule removal, two pieces of information will be displayed on the application.

First, the HSVD model is plotted along with the data and the residual. The macromolecule removed spectrum is also plotted. With these visualizations, you can qualitatively assess how well you picked your HSVD parameters, and how much of the residual water signal was successfully removed. If you are unhappy with the result, you can change the HSVD parameters, hit Run Macromolecule Removal again, and see the new results.

Saving the Results

Please note that these results are not saved to file until you hit the Save Macromolecule Removal Result button. Once you hit the button, a couple files will be saved:

• A .dat file with the suffix _hsvd. This file contains the HSVD model of the macromolecule signal.
• A sup.dat file. This file contains the metabolite only signal.