3T GE with unsupressed water: null for mMol/kg

[weberam2]

Hi William, Any idea why after processing my data with anatomical segmentation and water reference, I am getting null results for mMol/kg? Everything else looks good as far as I can tell (no errors...)

spec2nii ge ../P09216.7
fsl_mrs_preproc --output processed --data P09216.nii.gz --reference P09216_ref.nii.gz --report
fsl_mrs  --data processed/metab.nii.gz --basis LCModel_GE_UnEdited_PRESS_GABA35_.BASIS --output example_svs  --h2o processed/wref.nii.gz --tissue_frac segmentation.json --report

Cheers, Alex W.

[wtclarke]

HI Alex,

What are the values in segmentation.json? And what's in the quantifications section of the report?

[weberam2]

Hi William,

{     "CSF": 0.186333,     "GM": 0.62672,     "WM": 0.186948 }

And attached is the Quantification Information

Thanks!

Alex W.

[weberam2]

Hmm, not sure the image was attached when I replied by e-mail. Lesson learned

[wtclarke]

This was fixed after discussions on the MRSHUB forums. Spec2nii 0.4.6 now correctly interprets the timing parameters for GE sequences.