Hi Harriet

it's tough to diagnose from just this, but that is pretty bad! Can you give us some details about the editing? Or tar/gzip the whole subject dir and upload it and we will take a look

cheers Bruce On Tue, 24 Mar 2020, Harriet Cornwell wrote:

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Hello,

We are using FreeSurfer v5.3. and are sometimes finding that a brain can seem okay when it is first run through the recon-all process and is edited, but then when it is re-run the segmentation seems to deteriorate hugely. I have screenshotted an example below.

Are you able to advise us on why this might be happening and what we could do about this? One of the options I had thought about was to re-run the recon-all from scratch but it doesn’t seem very time efficient to do this for multiple brains. Any suggestions would be gratefully received!

Thank you.