That is just part of the way the long stream works. When you run a base subject, you have to spec all the cross tps that go into it. I agree, it is not elegant.

On 8/8/2021 8:03 PM, Eszter Boros wrote:

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Dear FreeSurfer Team,

I am working on a longitudinal pipeline and after correcting the Cross and generating the Base, I can still see some pial problems sometimes (on the Base). I read on the Freesurfer website that it is possible to correct and regenerate only the Base, but when I use this command:

recon-all -base OAS2_0057 -autorecon-pial

/where OAS2_0057 is the name of the Base/

I get the following error message:

ERROR: must specify subjects for base subject using -base-tp

Why is this not working? I am using Freesurefer 7.1.1. Thank you so much!

All the best, Eszter Boros

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