Hi Ken,

you should always look at the output from the …long.base directories, those are the final outputs. Looks to me that you are looking at the cross sectional produced surfaces from the first stage. Those will be - in different spaces (as the heads are in different positions in the scanner) - created independently and therefore will look more different from each other than the surfaces from the long stream.

Best, Martin

On 25. Sep 2020, at 15:55, Douglas N. Greve dgreve@mgh.harvard.edu wrote:

What is your command line for visualization? Can you also show the base image as an underlay?

On 9/24/2020 6:54 PM, KennethSPrice wrote:

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Hello, I am running a longitudinal study and am examining the pial surface for my 2 timepoints. The surfaces are slightly offset. Will this effect my statistical analysis for volume and thickness? I have attached the pial surface for each time point to this email. Should I be examining timpoint1.long and timepoint2.long instead?

Thanks, Ken

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