MTsat Values are higher than expected

SCT
1

I am trying to get the MTsat values in the cervical spinal cord. The values I am getting are much higher than expected.

I tried to enter the FA and TR manually instead of reading them from the .nii files, but this still results in the same values of MTsat > 5 (I have tried this for more than 25 subjects and am getting high values of MTsat for all, but MTR and WM values seem correct)

Here is an iCloud link to a control subject.

The scripts used to process this subject are in the folder: CanProCo/Cache/NIFTI/Vancouver
-mtsat_split.sh was used to split the original MTsat_ON_OFF-S scan into separate ON and OFF files

The subject files are in the folder: CanProCo/Cache/NIFTI/Vancouver/CAN-02-CON-005-M0/SPINE
-MTsat data from this patient is in the document CAN-02-CON-005-M0_MTsat.csv

2

Hi @Achopra,

Why are you expecting MTsat values <5? MTsat values from Philips scanner (which is your case) for the spine-generic project are around 5-6, see here.