Dear FS expersts!

I have two questions: 1) I am looking at the output from a FS run. When looking at the red and yellow lines it appears as the cortical thickness has bin estimated too thin. But when I take away the two lines and just look at the segmentation it looks quite god (and much thicker than the estimation of cortical thickness). How should I interpret this: Can it be that the cortical thickness measure is not completely correct while the cortical volumes from the segmentation is OK?

I have run this dataset in both 5.3 and 5.1 FS versions. To me it looks like the 5.3 is making the cortex even thinner than the 5.1.

In the 5.3 version I am using -mprage and -3T flags - while no flags was used in the 5.1 run. Is there any logical explanation for this?

Is there any trick to make affect the program so that the yellow line (white matter border) is more consistent with what I see in the segmentation.

Thanks in advance!

Erik