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wtclarke / fsl_mrs

Mirror of the FSL-MRS gitlab repository
https://git.fmrib.ox.ac.uk/fsl/fsl_mrs
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3T GE 35TE PRESS - TE "unusal value. Expecting a value < 0.5s" #13

Closed weberam2 closed 2 years ago

weberam2 commented 2 years ago

Hello! I have a P file that comes from a 3T GE scanner running a 35TE PRESS sequence

I run the following:

spec2nii ge P29696.7 fsl_mrs_preproc --output processed --data P29696.nii.gz --reference P29696_ref.nii.gz --report svs_segment -t T1.nii.gz processed/metab.nii.gz fsl_mrs --data metab.nii.gz --basis my_basis_spectra --output example_svs --h2o wref.nii.gz --tissue_frac segmentation.json --report

The basis set comes from MRSCloud https://braingps.mricloud.org/mrs-cloud

When I run fsl_mrs, it completes, but ends with: "te is an unusal value. Expecting a value < 0.5 s.
tr is an unusal value. Expecting a value < 20 s."

And in the report it says under Quantification Information:

"Metabolite T2: | 194.0 ms Metabolite T1: | 1.29 s Sequence echo time (TE): | 35000000.0 ms Sequence repetition time (TR): | 1500000.0 s Relaxation corrected water concentration: | 0 mmol/kg Metabolite relaxation correction (1/e(-TE/T2)): | inf Raw concentration to molarity scaling: | nan Raw concentration to molality scaling: | nan"

Any ideas? I'm happy to share my P file

wtclarke commented 2 years ago

Hi @weberam2,

It looks like the TE and TR get interpreted in the wrong units by spec2nii. This isn't entirely surprising as I don't have a huge amount of experience with GE p-files. Is there any chance you could share the file? I'll also take a closer look at the test cases I already have.

BW

Will

weberam2 commented 2 years ago

Pfile.zip Hi Will, Thanks for your help! I'm really stoked for fsl-mrs. You've done a great job. I sent you an e-mail, but will also upload a pfile here Good luck and let me know what you find... Cheers, Alex W.

wtclarke commented 2 years ago

Hi Alex,

This should be fixed as of spec2nii 0.4.6. It's up on pypi now (pip) but will take a few hours to get built and placed on conda-forge (conda).

BW

Will

wtclarke commented 2 years ago

Closing this issue. Feel free to reopen if the issue isn't fixed.