5tt_nocoreg.mif missing frontal cortex

[hollysullytoole]

The 5tt_nocoreg.mif I created is missing the frontal cortex and seems to be squished along the anterior-posterior direction. Any guesses what might have gone wrong? I have checked all of my input volumes (B0, T1, and all the co-registered versions) and they all look good.

[adsouza]

Hi Holly,
Check out the following post.

Challenges with Seed Generation using '5ttgen fsl' for Anatomically Constrained Tractography

Hi Kenbridge6, Running bias field correction on the anatomical image before 5ttgen fsl may help produce segmentations that are more accurate… I cannot guarantee that it will improve the segmentation quality, but might be worth a go Cheers, Arkiev

Does it happen systematically, or is this occurrence only in a single subject? Screenshots of the input T1 into 5ttgen might be helpful in identifying a solution

Hope this helps!

Cheers,
Arkiev