We acquired some SVS MRS test data of the left hippocampus at a 3T Prisma Siemens Scanner using a MEGA-sLASER protocol. I am currently trying to create a preprocessing pipeline using FSL-MRS. Now, I’d like to ask for your recommendations on the processing steps to perform. So far, I am doing the following based on the FSL-MRS practical (FSL-MRS Practical)
- Data Conversion of metabolite data and water reference data: Twix to nifti (spec2nii) which results in nifti files with the following dimension: metabolite data: 1,1,1,4128,32,2,64 and water reference: 1,1,1,4128,32,2,8
- Data splitting at DIM_EDIT (mrs_tools split): I split both the metabolite and water refrence data at DIM_EDIT, resulting in an ON and OFF spectrum of the metabolite data and the respective water references for each spectrum
- Averaging of both water reference files (fsl_mrs_proc average) from step 2
- Coil combination (fsl_mrs_proc coilcombine) separately for ON and OFF spectra from step 2 and for water references from step 2 using the averaged water references from step 3
- Phase-Frequency Alignment (fsl_mrs_proc align with --ppm 0.2 4.2) separately for ON and OFF spectra from step 4 and for both water references from step 4 (with --ppm 0 9)
- Data averaging (fsl_mrs_proc average) across DIM_DYN dimension separately for ON and OFF spectra and both water references from step 5
- Eddy current correction (fsl_mrs_proc ecc) separately for ON and OFF spectra from step 6 and both water references from step 6
- Removal of residual water (fsl_mrs_proc remove) for both water references from step 7
- Phase correction (fsl_mrs_proc phase) separately for ON and OFF spectra from step 7 and both water references from step 8
- Are there any problems with this approach that I may overlook? Or am I missing an essential step?
- At some point, I need to align the ON and OFF spectra and compute a difference spectrum. At which stage should that happen? And how would the respective commands look like in FSL-MRS (fsl_mrs_proc align?,fsl_mrs_proc align-diff?,fsl_mrs_proc subtract?)
- Is there any tutorial how to preprocess a MEGA sLaser sequence in general or even using FSL-MRS?
Thank you in advance!