External Email - Use Caution Hi Malte
Thanks. The Singularity version worked well! Simon ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Hoffmann, Malte,PhD <mhoffm...@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-YoHw8fIwSpH-bEfwIOQCX6cfs1vJbfdbD4-P1MOUmdJR-mxYRiyrEY7AoyKP42dtubIutdHbkah-psKktJkdzlmRi0NHPsnpe1iqAXpoVZqNO0XsmF6eAz_3WKJRUboxpxouS0Vv8RQbOJ9tXhp2pDw1k-Mhk2CmhDzD-g2yrxqQrUpdHpg-kmoufp1X0IqaOmuesBMJO1738gMefW3GANWWYBue4eKXQya67nAKjUwhNH8tKyvYj6rgbflk7xiKCIvOlIxX62wzk2f2iR/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fhub.docker.com%252Fr%252Ffreesurfer%252Fsynthmorph%26data%3D05%257C02%257Cspj24%2540universityofcambridgecloud.onmicrosoft.com%257Cc9790e1f7c864744d93a08dcf1f74acb%257C49a50445bdfa4b79ade3547b4f3986e9%257C1%257C0%257C638651291625445362%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%257C%257C%257C%26sdata%3DBoGRsMQ%252BwNwaF0o%252BvHDq3svDQCI3EiWOAWcW4TMeGBs%253D%26reserved%3D0<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-_FLqHgzgDiuVoUqCLWbn4X_NK7FGSwM_Wn-mzZvbK7pp5v01Z1bOPhc5RH602SQfiqDvikuDl1U25mEGI4lKDeQuivjJUrbVguXXI3c7TQmi1xid4hIwB775sC35EWtuS6hiUwNTrDZ8_fX6mJS07tpJ5kVeKWSNcqWctq6nkdAXcBFTeyqbVEd8n4ooObcxR1YPb76wWw5GvU_cQQ4B7fNx2l4c_7_Utx_mPLlvC1wwvz0yct2A3XcmoBsVRQ6qgYjpt5MeIsrTPNNevD-RtR6vHwd/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Fpub%252Fdist%252Ffreesurfer%252Fdev%252Fstable%252F%26data%3D05%257C02%257Cspj24%2540universityofcambridgecloud.onmicrosoft.com%257Cc9790e1f7c864744d93a08dcf1f74acb%257C49a50445bdfa4b79ade3547b4f3986e9%257C1%257C0%257C638651291625483969%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%257C%257C%257C%26sdata%3DkBcAk93kkWmUH3A2mk0iMLidWRF%252BIL3jtXipabbvZto%253D%26reserved%3D0<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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Simon Jones <sp...@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? 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