External Email - Use Caution        

Hi Malte

Thanks. The Singularity version worked well!

Simon
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Hoffmann, Malte,PhD <MHOFFMANN@MGH.HARVARD.EDU>
Sent: 21 October 2024 6:38 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_synthmorph regularisation
 
Hi Simon,

The SynthMorph version in FreeSurfer 7.4.1 only supports a fixed regularization value of 1. For more adjustable regularization via the `-r` flag (and improved registration overall), I recommend the latest SynthMorph from the Docker Hub. We distribute a script that supports Docker, Podman, Apptainer, or Singularity: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhub.docker.com%2Fr%2Ffreesurfer%2Fsynthmorph&data=05%7C02%7Cspj24%40universityofcambridgecloud.onmicrosoft.com%7Cc9790e1f7c864744d93a08dcf1f74acb%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638651291625445362%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=BoGRsMQ%2BwNwaF0o%2BvHDq3svDQCI3EiWOAWcW4TMeGBs%3D&reserved=0

Alternatively, you can download a stable dev build of FreeSurfer, which includes the latest SynthMorph: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Fstable%2F&data=05%7C02%7Cspj24%40universityofcambridgecloud.onmicrosoft.com%7Cc9790e1f7c864744d93a08dcf1f74acb%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638651291625483969%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=kBcAk93kkWmUH3A2mk0iMLidWRF%2BIL3jtXipabbvZto%3D&reserved=0

Best wishes,
Malte

________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Simon Jones <spj24@cam.ac.uk>
Sent: Monday, October 21, 2024 13:20
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_synthmorph regularisation

        External Email - Use Caution
Dear all

I tried to use change the regularisation parameter of mri_synthmorph using -s option in Freesurfer 7.4.1 but this option does not seem implemented. Is there a way to reduce the amount of regularisation?

Thanks for your help,

Simon


****************************************************************
Mr P Simon Jones
Research Associate
Department of Clinical Neurosciences
University of Cambridge
Herchel Smith Building, Forvie Site
Robinson Way
Cambridge Biomedical Campus
Cambridge CB2 0SZ UK
****************************************************************



_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=05%7C02%7Cspj24%40universityofcambridgecloud.onmicrosoft.com%7Cc9790e1f7c864744d93a08dcf1f74acb%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638651291625504300%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=YvHYfdMVw04QWrVbSWySG5gVn1PqEhuvYm2hJppr2fQ%3D&reserved=0
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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline&data=05%7C02%7Cspj24%40universityofcambridgecloud.onmicrosoft.com%7Cc9790e1f7c864744d93a08dcf1f74acb%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638651291625521464%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=weKg4WW6CpXg55WyFF17F4CdCP5k57iZR1gBAJ%2FCA6M%3D&reserved=0 <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline&data=05%7C02%7Cspj24%40universityofcambridgecloud.onmicrosoft.com%7Cc9790e1f7c864744d93a08dcf1f74acb%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638651291625538448%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=P1SWGJ%2Bt3NG0xTFqmmgMf637m1OiqCTK0xhOkE%2FLJ3w%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.