5tt error

Hello I hope all is well. I am currently experiencing some issues with 5ttgen fsl. Information: all of the images have been preprocessed with the same pipeline. For the majority of images, the 5tt image is successfully generated. In some of the images during 5tt processing the following error occurs. Could this be an image quality issue or an issue from arising from the scanner? Any insight is greatly appreciated.

Hi Ricardo,

The erroneous warning message formatting means that you are using a version of MRtrix3 prior to 3.0.0, since it was resolved here.

The issue has been discussed multiple times on the forum; see e.g. this thread. It’s not something to be overly concerned about, but you can check the locations of such errors using the 5ttcheck command and quantify the sum of tissue fractions using mrmath sum -axis 3 to see the magnitude of the problem; if the errors are ~ 0.1 or smaller then tracking shouldn’t be affected. This would also likely not appear at all if using an up-to-date installation (or if it does appear it’s a handful of voxels at most).