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Hi!

So, basically what is happening is the white matter and pial surfaces are not aligning up correctly on any of the slices. The white matter surface isn’t outlining white matter, which is causing the pial to not outline the pial. It almost looks like the pial is outlining the wm surface that is how off it is. The aseg.mgz is just as bad. I converted the imagine to a pdf hopefully you can view it better.

On Tue, Oct 27, 2020 at 4:05 PM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote: It is a little hard to see what is going on, but the image looks pretty blurry. How does the aseg.mgz look?

On 10/24/2020 2:33 PM, Sierra Ann Jarvis wrote:

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Hello FreeSurfer Developers,

I am attempting to run this subject through a longitudinal process. I have successfully ran and edited the cross-sectional and the .base. My problem occurs when I run the .longs. I do not receive an error in the recon-all.log, but the surfaces on the image when I pull it up on FreeView are very jumbled. Below I have attached a screenshot of a coronal slice to give you an idea of what I am dealing with.

I ran the subject through: recon-all -long sub_post/ sub.base -all

FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Recon-all log last line: recon-all -s sub-5504_post.long.sub-5504.base finished without error at Fri Oct 16 13:44:10 MDT 2020

Thank you for your time, Sierra Jarvis

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