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Dear Team, We are currently using the new SuperSynth method to process and segment 3T T1-weighted MRI volumes acquired at three longitudinal time points (Baseline, Visit 1, and Visit 2). We would like to know whether it is possible to perform a longitudinal analysis using the outputs generated by SuperSynth. If so, could you please describe the recommended workflow or commands to follow? Specifically, we are interested in the following:
* Can SuperSynth outputs be used for longitudinal processing across multiple time points? * Is there a recommended pipeline or set of commands for longitudinal analysis? * Can we generate cortical thickness measurements and cortical thickness maps to visualize brain changes over time? * Are there any additional recommendations or best practices for performing longitudinal structural analyses using SuperSynth, SynthSeg or recon-all-clinical outputs?
Any suggestions, documentation, or example of workflows would be greatly appreciated. Thank you for your time and assistance. Best, Ajay
Dear Ajay,
Please take a look at this paper (which is based on SynthSeg, but SuperSynth is essentially the same method with more outputs and better training data): https://www.sciencedirect.com/science/article/pii/S1361841525002099
In short:
* You can run SuperSynth on the timepoints independently, and it does a pretty good job already. * You can get segmentations that are longitudinally a bit cleaner by running USLR on top (see the aforementioned paper). * SuperSynth does not currently have a cortical stream.
Best wishes,
/Eugenio
-- Juan Eugenio Iglesias http://www.jeiglesias.com From: Ajay Sharma ashar126@jh.edu Date: Thursday, July 9, 2026 at 2:23 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] SuperSynth Method and Longitudnal Analysis
External Email - Use Caution Dear Team, We are currently using the new SuperSynth method to process and segment 3T T1-weighted MRI volumes acquired at three longitudinal time points (Baseline, Visit 1, and Visit 2). We would like to know whether it is possible to perform a longitudinal analysis using the outputs generated by SuperSynth. If so, could you please describe the recommended workflow or commands to follow? Specifically, we are interested in the following:
* Can SuperSynth outputs be used for longitudinal processing across multiple time points? * Is there a recommended pipeline or set of commands for longitudinal analysis? * Can we generate cortical thickness measurements and cortical thickness maps to visualize brain changes over time? * Are there any additional recommendations or best practices for performing longitudinal structural analyses using SuperSynth, SynthSeg or recon-all-clinical outputs?
Any suggestions, documentation, or example of workflows would be greatly appreciated. Thank you for your time and assistance. Best, Ajay
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Many Thanks Eugenio,
Great work. Helpful.
Best, Ajay ________________________________ From: Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Sent: Thursday, July 9, 2026 5:21 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: SuperSynth Method and Longitudnal Analysis
External Email - Use Caution
Dear Ajay,
Please take a look at this paper (which is based on SynthSeg, but SuperSynth is essentially the same method with more outputs and better training data): https://secure-web.cisco.com/1oqOSIHgEmZucDvVmEhdEt6xiE0bJbSnCY3SXogkgTAZmkp...
In short:
* You can run SuperSynth on the timepoints independently, and it does a pretty good job already. * You can get segmentations that are longitudinally a bit cleaner by running USLR on top (see the aforementioned paper). * SuperSynth does not currently have a cortical stream.
Best wishes,
/Eugenio
-- Juan Eugenio Iglesias http://secure-web.cisco.com/1vVeh70LRG748X5oDkK3A5GbIxdFCGt7UA5_Y4q--72nel8e... From: Ajay Sharma ashar126@jh.edu Date: Thursday, July 9, 2026 at 2:23 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] SuperSynth Method and Longitudnal Analysis
External Email - Use Caution Dear Team, We are currently using the new SuperSynth method to process and segment 3T T1-weighted MRI volumes acquired at three longitudinal time points (Baseline, Visit 1, and Visit 2). We would like to know whether it is possible to perform a longitudinal analysis using the outputs generated by SuperSynth. If so, could you please describe the recommended workflow or commands to follow? Specifically, we are interested in the following:
* Can SuperSynth outputs be used for longitudinal processing across multiple time points? * Is there a recommended pipeline or set of commands for longitudinal analysis? * Can we generate cortical thickness measurements and cortical thickness maps to visualize brain changes over time? * Are there any additional recommendations or best practices for performing longitudinal structural analyses using SuperSynth, SynthSeg or recon-all-clinical outputs?
Any suggestions, documentation, or example of workflows would be greatly appreciated. Thank you for your time and assistance. Best, Ajay
freesurfer@nmr.mgh.harvard.edu
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Ajay Sharma -
Iglesias Gonzalez, Juan E.