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Thank you so much! This was very helpful. I did not know that the command will respect my edits. For some reason, this did not happen for one of the subjects, and it looked like that the command completely regenerated the base. But it worked when I tried again with a different subject.

All the best, Eszter Boros

Douglas N. Greve dgreve@mgh.harvard.edu ezt írta (időpont: 2021. aug. 18., Sze, 22:06):

That command will re-run the base, but it should respect your edits. Is that not the case? If you just want to re-run part of it, you can specify the stage (eg, -autorecon2) instead of -all

On 8/18/2021 8:05 PM, Eszter Boros wrote:

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Thank you for your answer!

I think I should clarify this question a little bit. So this is about correcting the Base. And run recon-all *after *correcting the Base. What command should I use here? if I want to regenerate only the Base after correcting it?

Because the common below does not work: (ERROR: must specify subjects for base subject using -base-tp) recon-all -base OAS2_0057 -autorecon-pial

But if I use "recon-all -base OAS2_0001 -tp OAS2_0001_MR1 -tp OAS2_0001_MR2 -all" that just creates a new Base based on the cross MR1 and MR2.

My question is how can I regenerate the corrected Base? What command should I use?

Thank you so much!

All the best, Eszter Boros

Eszter Boros boros.eszter0226@gmail.com ezt írta (időpont: 2021. aug. 8., V, 19:04):

...

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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