Here is the tutorial page for longitudinal pipeline - https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing

 

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

 

 

 

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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