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 ****************************************************************

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