External Email - Use Caution

Here is the tutorial page for longitudinal pipeline - https://secure-web.cisco.com/1DcUJ0a_skONZSHVRpSGkgbTHuJUYN0f05kxjKkGh8ULxXW...

In step 1 (cross), recon-all -all -s <tpNid> -i path_to_tpN_dcm you should have processed each of your time points separately, for example, <tpNid> = tp1, tp2, tp3 (these are the subjectIDs you choose for your subject/timepoint). In step 2 (base), recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all 1. Choose an unique subjectID as your <templateid> (for example, base_tp1_tp2_tp3). 2. -tp <tp1id> ... are the subjectIDs (tp1, tp2, tp3) from your cross process. In step 3 (long), 'recon-all -long <tpNid> <templateid> -all'. It should output in directory <tpNid>.long.<templateid>.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Atwater, Emanuel R Sent: Thursday, July 27, 2023 6:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] (no subject)

External Email - Use Caution Hello FreeSurfer Team,

I recently messaged about running a longitudinal scan on a couple of images.

The response told me to utilize "timepoints": For base processing, specify each timepoint with -tp <> (not the nii file). recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all

I've attempted to review the youtube videos and instructions made available online but am unsure what "timepoints" are. Can I have some clarification on what exactly a timepoint is, please.

FS version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b Recon-all.log: see attached

V/r, Emanuel Atwater