Hi @ThomasCawood,
@Helge’s suggestions are all good… however, specific to the FSL-MRS case: just glancing through your document, I think the problem lies in your original basis set conversion. You should be seeing an NAA peak around 2 ppm, and a Cr peak around 3 ppm – but your figures (reproduced here) show NAA around 3.4 and Cr around 3.8. To me this indicates an incorrectly specified dwell time somewhere in the process.
See also the comment thread here
When running basis_tools convert, the --bandwidth parameter should describe the bandwidth of the input basis set (it’s not contained in the lcmodel RAW file headers), not your target data. So, try this:
basis_tools convert RawBasis_for_PRESSSiemens_TE_35_BW_2500_NPts_1024 --bandwidth 2500 --fieldstrength 3.0 basis_converted
A secondary issue, your reduced basis set is missing NAA. This isn’t your main problem right now, but it should be fixed before you go too much further.
You also mention in the document,
MRI scanner data processed using (done in a shell script):
• Conversion of dicoms to nifti [spec2nii dicom -f converted_${b} *.dcm]
If you’re starting with DICOM files, a number of the other preprocessing steps may be redundant… this would explain some of the other preprocessing issues you mention therein. You’ll have a lot more flexibility if you work with TWIX (.dat) files instead. Again, it’s not your main issue at the moment but it could be something to look into…
Alex.