Dear Tamara,

I presume that you edited your reconstruction in "Long" (=3rd) stage of longitudinal stream (recon-all -long )?.

If this is the case, I think that you can use

recon-all -long tpN1 templateID -autorecon2-wm -autorecon3

or

recon-all -long tpN1 templateID -autorecon2-noaseg -autorecon3

(effectively both commands are equivalent, they run the same steps).

where tpN1 is name of your directory defining cross-sectional recon (1st stage) and templateID is name of directory of your base (created in stage 2).

See
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#RerunningEditsCommands

Regards,

Antonin Skoch


Hello,

After I make edits to my aseg output in the longitudinal stream, do I just
run the following command to recreate the final volumes:

recon-long -autorecon2-noaseg -subjid <Subj_ID>

I assume the -subjid is the name of the edited time point and <Subj_ID> is
the name of the recreated volumes?

Thank you,
Tamara