Oh, I see. They are fairly different in the way that they try to place cortical surfaces. Recon-all uses T1 intensities directly, and only works with high-resolution near-isotropic T1w scans. Recon-all-clinical uses machine learning and is compatible with scans of any contrast and resolution, BUT is less accurate than recon-all if you actually do have 1mm T1 data. So, I would try recon-all first.

Cheers,

/Eugenio

Juan Eugenio Iglesias

http://www.jeiglesias.com

From: Stefanie Bradley <stefanie.bradley@mail.utoronto.ca>
Date: Wednesday, July 2, 2025 at 09:24
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: Recon-all clinical vs. FS version 8.0.0

External Email - Use Caution

Hi Eugenio,

Thanks for your response.

I was more wondering if the standard recon-all pipelines (v8.0) are the same for recon-all clinical, since it seems like recon-all in version 8 uses Synthseg by default.

My population is children aged 4-6 years old with cerebral palsy. The T1-weighted scans are MPRAGE, 0.8mm isotropic.

Thanks,

Stefanie

From: Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu>
Sent: Tuesday, July 1, 2025 8:35 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: Recon-all clinical vs. FS version 8.0.0

Dear Stefanie,

What type of pathology are we discussing? What ages? What MRI sequence and resolution?

Cheers,

/Eugenio

Juan Eugenio Iglesias

http://www.jeiglesias.com

From: Stefanie Bradley <stefanie.bradley@mail.utoronto.ca>
Date: Tuesday, July 1, 2025 at 5:49 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Recon-all clinical vs. FS version 8.0.0

External Email - Use Caution

Hi there,

I am analyzing some pediatric brains with clinical pathology, and I was wondering if I would expect a difference in the reconstructions from regular recon-all (Freesurfer version 8.0.0) vs. recon-all clinical, since they both use SynthSeg from what I understand?

Thanks,

Stefanie