FSL-MRS with 3T GE Discovery: TE and TR are orders of magnitude off


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…

Please help

Alex W.

Hi Alex,

Before @wclarke rolls in and clarifies whether this is a spec2nii thing - can you open the .basis file in a text editor and check what it says for ECHOT? I just want to make sure it’s not related to MRSCloud.


Hi Georg,

The MRSCloud basis file says: “ECHOT = 35.00,”


Alex W.

1 Like

Hi All,
William fixed this for me. If anyone else is experiencing this problem, it update your spec2nii to the most recent version (at least 0.4.6)
pip install spec2nii==0.4.6