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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