That’s not easy to do out of the box, because you would need to run SynthSR before PreFreeSurfer, when normally you do the reverse. Not having T2w scans just means you would need to enable legacy mode options.

I have some code that imports a SynthSR result into HCP Pipeline structures, though SynthSR is rapidly changing and each time it changes I have to update that import code. Perhaps I can share it once things have stabilized.

Matt.

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of KennethSPrice <KennethSPrice@protonmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, August 3, 2023 at 12:30 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] using synthsr with HCP Pipeline

External Email - Use Caution

Hello all,

I am currently struggling through the HCP Pipeline! I want to use clinical scans processed with synthsr in the HCP Pipeline.

1.) Is this even possible?

2.) Is there a way to get a T2 output with synthsr?

3.) In lieu of the HCP Pipeline, could you use SythSR scans with the HCP Database to do a normal group analysis?

Thanks,

Ken

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