External Email - Use Caution        

Please unsubscribe me! 

Dr Sunniva Fenn-Moltu (she/her)

Postdoctoral Research Associate


Department of Forensic and Neurodevelopmental Science
Institute of Psychiatry, Psychology & Neuroscience
King’s College London

16 De Crespigny Park, Denmark Hill, London, SE5 8AF


From: freesurfer-request@nmr.mgh.harvard.edu <freesurfer-request@nmr.mgh.harvard.edu>
Sent: 02 July 2025 15:23
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Freesurfer Digest, Vol 257, Issue 14
 
Send Freesurfer mailing list submissions to
        freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via email, send a message with subject or
body 'help' to
        freesurfer-request@nmr.mgh.harvard.edu

You can reach the person managing the list at
        freesurfer-owner@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."

Today's Topics:

   1. Re: Recon-all clinical vs. FS version 8.0.0
      (Iglesias Gonzalez, Juan E.)


----------------------------------------------------------------------

Message: 1
Date: Wed, 2 Jul 2025 14:23:09 +0000
From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edu>
Subject: [Freesurfer] Re: Recon-all clinical vs.  FS version 8.0.0
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:  <PH0PR04MB83888D5F6E0D1EB14A99250EFD40A@PH0PR04MB8388.nam
        prd04.prod.outlook.com>
Content-Type: multipart/alternative;    boundary="_000_PH0PR04MB83888D
        5F6E0D1EB14A99250EFD40APH0PR04MB8388namp_"

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
https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jeiglesias.com%2F&data=05%7C02%7Csunniva.fenn-moltu%40kcl.ac.uk%7C31c3752bbb93455eeefb08ddb97409a1%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638870630244364781%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=CQAbsRQi3TBKEZ8CXxyn9%2FU1AlqVxfv25KlLMT0gL%2BU%3D&reserved=0

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

https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jeiglesias.com%2F&data=05%7C02%7Csunniva.fenn-moltu%40kcl.ac.uk%7C31c3752bbb93455eeefb08ddb97409a1%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638870630244384054%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=sUAYvPOGHhin%2FMUV9g6gMTGgIh99M3YZsnYM1ZWExjg%3D&reserved=0



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






-------------- next part --------------
A message part incompatible with plain text digests has been removed ...
Name: not available
Type: text/html
Size: 9120 bytes
Desc: not available

------------------------------

Subject: Digest Footer

_______________________________________________
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu
To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu
https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F&data=05%7C02%7Csunniva.fenn-moltu%40kcl.ac.uk%7C31c3752bbb93455eeefb08ddb97409a1%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638870630244397261%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=lK%2FPJ3MBoB29GRzr9ixmBSEHE7V%2B0HYx7SoVqYVrJew%3D&reserved=0


------------------------------

End of Freesurfer Digest, Vol 257, Issue 14
*******************************************
The information in this e-mail is intended only for the person to whom it is addressed.  If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline&data=05%7C02%7Csunniva.fenn-moltu%40kcl.ac.uk%7C31c3752bbb93455eeefb08ddb97409a1%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638870630244410306%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=tEIlGZoQXF9QDUv12MDJQ5JsRY4LmghULbXq77MnpjY%3D&reserved=0 <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline&data=05%7C02%7Csunniva.fenn-moltu%40kcl.ac.uk%7C31c3752bbb93455eeefb08ddb97409a1%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638870630244423130%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=STxhNhKQZKF0M4mPGsyGxmUOv3rq8hHJ7iLEVm4MwRg%3D&reserved=0> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.