Thanks for the suggestion. I actually used fsl_mrs_preproc for this dataset. As I mentioned in my previous threads (Error in FSL-MRS Quantification: "Specified metabolite isn't in the list of basis spectra" and MEGA-PRESS Edited Sequence Subtraction in FSL-MRS).
Thank you for your reply. I actually already ran the segmentation, so I will use that data for statistical analysis and QC