Dear Barbara,
you could in principle use recon-all-clinical for the enhanced T1 but the surface reconstruction would probably fail.
Instead, I’d probably run SynthSR to synthesize 1mm T1 intensities while inpainting abnormalities and then run the standard recon-all.
Cheers,
/Eugenio
http://www.jeiglesias.com
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Barbara Bellenberg <Barbara.Bellenberg@ruhr-uni-bochum.de>
Date: Thursday, June 13, 2024 at 3:30 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] recon-all clinical : usage with contrast-enhanced T1-weighted images?
External Email - Use Caution
Dear all,
I would like to use the recon-all-clinical pipeline with Gadolinium
contrast-enhanced 3D-T1 weighted images. Can you tell me if
recon-all-clinical is suitable for this purpose?
Thanks in adcance for your support!
Barbara
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