For base processing, specify each timepoint with -tp <> (not the nii file).

recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Atwater, Emanuel R
Sent: Wednesday, July 5, 2023 11:37 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal Pipeline Issue

External Email - Use Caution

Hello Freesurfer Team

I’m attempting to create the base for the longitudinal scan process, as described in the Longitudinal Tutorial (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial), but for some reason I am unable successfully complete the base.

FS version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b

Recon-all.log: see attached

V/r,

Emanuel Atwater