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

-- Juan Eugenio Iglesias 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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