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: https://secure-web.cisco.com/1T-3qjNZHZVdbQXaud6ssZABmPOZzEGiBfEcyGi0kJDVjN-...https://secure-web.cisco.com/1E65ecLrSuu9F69GhsJhkBkUod5yOfd_kFY4cB_RyFaFxWKORsp_nzbtQMlBbda7arcgTU5fgMZjwBAi5TY6xQPS38LrLl6cEO0KiDasAnlPtsgl5AznqroohQFOdzSsubOLpJrx9VlY5qcHSdDutySJGtykRXtp398rzLYZp8urNi4W5udGRYytaREJc85w1sVhtN8vS-WYVREVY4BqENKgXHvgseUrkXSNz4o6V1hta7NpQeSmCttOpT8RaEP88DMYzabnMvTjOaH7UR6UOblXIkdZKMGYhJbysYzP2DLU6dApXWQDrFv-GQSbdVLdo/https%3A%2F%2Fhub.docker.com%2Fr%2Ffreesurfer%2Fsynthmorph
Alternatively, you can download a stable dev build of FreeSurfer, which includes the latest SynthMorph: https://secure-web.cisco.com/1yQ5pTa_MLr_pJtLHIj7FSKfxluQimDKnQSuM-_FLqHgzgD...https://secure-web.cisco.com/1wASHEixBgnJfLIl91J9AOppLMgpkbEdOTQxVI9e7QcAGr9xT0pTbTQ2nITJQgxaBhsualnJvbRlu4GUMQxY_ojUvXvUai1NXFXZXb3sEHEKpxWFLEcmhhKwIgf7joWpQ1ZimwrU68sFxUdIBWF7tBdlbzUpL-QDHR7jVt-BzG5rrjbbwzGEYLGSZZQ-Fzv8lWqoIFVD87Spd32CmJ0wggrMB25u2VN_-gp8Kh0b-pSF0cELA2C_GTUs3NiFsP-xBmrz4iExGbskmVfKScvEqT-73fqhmrHOu-3l7---mohG7I9K0_C3zW0zFs2gVU41F/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Fstable%2F
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 https://secure-web.cisco.com/1PnEbax8StNpqeB73EC3CKtlLQwTXoLAvitmiT6hspuw13a...https://secure-web.cisco.com/1qDrHiOAt7crISIZ8Za4RMNMWAvEIOAE99K1YtZcwjer0zU-y7F7KmXoqHc0-9Ang6M2bXZ27jtTDTNobpzzK6rfciYArv6J6WQi0JJsJ0yrxR_2TT2_nq2eIpQh4OgYr6QyfnrHcl6AFNOAPDq5c8eZzCbMxFfnEOrEYJVIhiKOTSz6CaW6DaeEjiJ9jKjg81R2KYgHfBZxhJyfvOHHAdhylrQbgR1tsMvXRFUg3b9V-b91a-FkfhfOWfHCyGLVFNQqF2lkACE1nhHX1vVvEXlDqeENMpctmtzp7ppaFBhu1vbOHhhze4PtVS7XhJIXl/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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://secure-web.cisco.com/1B0DNn55ob1nNnDgiuQdoPErXT1tmw-0jOTsbyk3zHS744w...https://secure-web.cisco.com/1XJ5eTOK70ZBCn3YZwMrf6GfmEbNXksugr2884yykd8Ub1Igw7Y24mgAv-bVOIGq18k3WW03ltFkbK506khCXbf4Ews_62zeJZJuc-G4CBuYzukK2DL7dV5a_d9Natr8ic95z_NNw_TtSyRbJu-hoDZL-srWrAgEQOOSL4Vi4BWxcOYuCoqO2HZ6gm6_Uykx_NCULEgAwlOhOX3aPu9DMXSR-JnzSr9dEsQ4M3zpHUdX6NbXojwarunaqN-ttGtADWJ6rgJOHgo7gp6zgRJ_a6ZM2ed7-L3U14c0mW7Zh8QdkDhGKHQneXA2ZI2dgRd0M/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <https://secure-web.cisco.com/1jWLXSY4kKXRh9zn7uS5DvOokcrMSSuLRsIK1jHPMQScbCA...https://secure-web.cisco.com/1XJ5eTOK70ZBCn3YZwMrf6GfmEbNXksugr2884yykd8Ub1Igw7Y24mgAv-bVOIGq18k3WW03ltFkbK506khCXbf4Ews_62zeJZJuc-G4CBuYzukK2DL7dV5a_d9Natr8ic95z_NNw_TtSyRbJu-hoDZL-srWrAgEQOOSL4Vi4BWxcOYuCoqO2HZ6gm6_Uykx_NCULEgAwlOhOX3aPu9DMXSR-JnzSr9dEsQ4M3zpHUdX6NbXojwarunaqN-ttGtADWJ6rgJOHgo7gp6zgRJ_a6ZM2ed7-L3U14c0mW7Zh8QdkDhGKHQneXA2ZI2dgRd0M/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.