Assignment 2: Semi-quantitative brain spectroscopy

Please conduct and describe gray matter brain spectroscopy. The practical part is discussed on the course homepage under "Data acquisition". The analysis part was discussed in connection with exercises in prior weeks. Use the software developed and validated during these.

Use the spectroscopy data acquired during your own exercise, or another group's data from this year. The acquisition parameters are in the files. Code to read data is provided on DTU Learn. Help to find, read and interpret files is offered.

Document the acquisition, analysis and findings in a minimal, but informative form as described on the course homepage under "Assignments" (same guidelines as for the first exercise). Please supply the employed software so useful feedback can be provided. Only the report is graded, not the attached software.

Show and describe the voxel location and corresponding spectra, the fit and the residuals in the frequency range of interest. Use assumptions about the water concentration in tissue, and about the relaxation times of water and metabolites to measure NAA, Choline and Creatine concentrations (see spectroscopy review article and note on quantitative spectroscopy on DTU Learn).

Comment on the quality of the fit and on non-modelled spectral features (they are unavoidable but may not offset the metabolite measures much, if small).

Comment on the rather severe potential sources of error in the analysis (more elaborate measurements, analysis and quality control is typically employed, but this is beyond the course).

Include the key mathematics. Submit PDF-format.

The general advice for Assigment 1 also applies to this report. Further advice in Learn/Content/ReportInfo, and on the course homepage (different kinds of advice in the various places). A message is sent via DTU Learn if there are significant changes to the texts.