External Email - Use Caution
You can run longitudinal analysis with 2 timepoints -
https://secure-web.cisco.com/1jQQ0cVi7lI0yGhk44hY2J-io2CWVn1H8Pa0LTIgv7lJoY6DvAzdL-94yJFuUJgiTBTy90dccfUzUHS74CitHvEMQPm31joNosyoZGVcpO0GnFgFpHpm-PYiOjWcw_hH1AS_OZXMTT517S1fM6Ldxek4-QJbcuzYXEjTS-R732JLE0qhJmEjSCM9vSs9SNgadFwCKjstoQAknqe3BybCgxS4-OdJI2F8eKz2o3nwvxUZDkEcBJPIM_KA7AcelwhFM/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalProcessing
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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.
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