5ttgen hsvs - failing to segment regions

Hi all,

So for one case 5ttgen hsvs isn’t correctly segmenting GM/WM/etc. So far I’ve tried running this case on two different machines and tried re-running freesurfer a few times. I’ve attached T1 images with the 5tt image overlaid. Anyone have any idea whats going on?

Thanks in advance for any guidance!

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Hi Lawrence,

I’ve never seen a result like that. Only hint is that the value of the overlay 5TT image is reported as “?”, meaning most likely the location of the cursor is actually outside of the FoV of that image. Showing mrinfo for both the T1w and the 5TT image might show something, but probably not enough; more likely I’d need to get the data from you and try to reproduce so that I can go digging for the root cause.


Hi Rob and Lawrence,

Was there a solution to this unusual result? I am experiencing something similar, also just in a handful of subjects.


Hi Adsouza,

Thanks for replying on this topic and sorry for the no reply rob, I started replying and then forgot to hit send! I was unable to solve this and I’m unable to share the data as unfortunately it is patient data. Annoyingly when using the HCP or publicly available data I haven’t run into any cases where this has happened. Perhaps someone in the future will and be able to share the data!

All the best,