External Email - Use Caution

You can run longitudinal analysis with 2 timepoints - https://secure-web.cisco.com/1jQQ0cVi7lI0yGhk44hY2J-io2CWVn1H8Pa0LTIgv7lJoY6...

For base processing, the command will look like this recon-all -base <templateid> -tp <tp1id> -tp <tp2id> -all

<templateid> needs to be an unique identifier in your SUBJECTS_DIR.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of KennethSPrice Sent: Tuesday, April 18, 2023 7:08 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] is it possible to run a longitudinal study on 2 "-base" images?

External Email - Use Caution Helloo,

I have 2 sets clinical scans on a single subject that I put through Synth_SR. The Synth_SR tutorial suggests that if you have T1, T2, and FLAIR scans, you might want to average the number of voxels when doing ROI analysis. I want to apply this logic to cortical analysis.

My idea is to "average" the cortex of T1, T2, and FLAIR scans from year 1 and year 2 using the longitudinal pipeline. Then I'd like to compare the "-base" images from both sets. Previously, when I've tried using the "-base" images in a study, I get the error that says something to the effect of "It appears that this subject ID is an existing base/template from longitudinal processing (-base): xxxx. If you are trying to re-run a -base template you need to pass the -base and all -tp flags:...."

So, is it possible to do a longitudinal analysis on 2 "-base" images, or is there a different method you might suggest?

Thank you all.