5ttcheck error


There are warnings when 5ttgen.
Here are my commands:

5ttgen fsl T1w_bet.nii.gz 5tt_nocoreg.mif -premasked

and the warnings:

5ttgen: [WARNING] Generated image does not perfectly conform to 5TT format:
5ttgen: [WARNING] 5ttcheck: [WARNING] Image "result.mif" contains 8 brain voxels with non-unity sum of partial volume fractions
5ttgen: [WARNING] 5ttcheck: [WARNING] Input image does not perfectly conform to 5TT format, but may still be applicable (suggest re-running using the -masks option to see voxels where tissue fractions do not sum to 1.0)

what may cause this? How can I ensure these errors whether influence the following tractography?


Hi @hyting,

You’ll find others have reported similar issues on the forum. Perhaps the most relevant answer is this one from @rsmith, but I recommend you have a search for that error message on the forum and see what others have done about it.


Thank you @jdtournier .

This is very helpful. And thank you for your suggestion, I’ll have a search on the forum before next time. :smiling_face: