I am trying to process some P files from a 3T GE Discovery.
The sequence is a PRESS 35TE
I am also trying to use FSL-MRS
So far my code looks like this:
spec2nii ge P09216.7 fsl_mrs_preproc --output processed --data P09216.nii.gz --reference P09216_ref.nii.gz --report svs_segment -t ../../../sub-Pilot01/anat/sub-Pilot01_T1w.nii.gz processed/metab.nii.gz fsl_mrs --data metab.nii.gz --basis LCModel_GE_Unedited_PRESS_35_.BASIS --output example_svs --h2o wref.nii.gz --tissue_frac segmentation.json --report
The basis file comes from MRSCloud
Everything goes well until the ‘fsl_mrs’ when it completes the analysis but says:
te is an unusal value. Expecting a value < 0.5 s.
tr is an unusal value. Expecting a value < 20 s.
When I look at the report, it seems to think TE is 35000000.0 ms and TR 1500000.0 s
Maybe this is happening at the spec2nii stage? My version is 0.4.4
I can’t seem to find any mention of TE or TR using something like ‘fslhd’ to look at the nifti files…