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:
External Email - Use Caution
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 mailto: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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer