External Email - Use Caution Dear Freesurfer Experts,
I am looking into generating subcortical surfaces from the subcortical volumes generated from recon-all. The reason for this is I am trying to create a vertex based Morphological Similarity Network generated from both cortical and subcortical regions. Ideally I would avoid Volume Based Statistics as, from what I can see, I am limited to just thickness features. I have run recon-all for all of my participants, and ideally my set up for surface subcortical features would be done in freesurfer as well, although I am aware of other tools such as: https://secure-web.cisco.com/1Naw6TVmVSgW4iHi_BvEcAItpkOmdAs3fMgTWn1abKwPfBB8rdZFU3uvsi4cPqx3S8bYQkyU527GS0tUWq5iTLIxi4h-neYTg3rRF4rm36g6ssGYvZTHYISx4xuiaDvdlgjLf00reXO6y4TRF6SOjlA2eclFajGQaaMj_WAPMydblg1WhHM3s49fAVOEYVpYz5DKxrM9HaIEbEhAUQfic1RPJW9C_WvN7qtqqxCGA2jBE5sAQ3gQdaiTi6ckB5Co2EaKd_919kOa34WJ6MXeQhIRrDU18ASd_y1u_AhvG__WBnPhcjqAzmFXgwtAXFQUeuXxMG33RICOWUxpS-QpFhg/https%3A%2F%2Fgithub.com%2FNIRALUser%2FSPHARM-PDM%3Ftab%3Dreadme-ov-file https://secure-web.cisco.com/1u1Ru_EifdWYQsjg7F-GHFGBp-Vkvjk_3iHSqwgV0CTWKwS_FdITj126INHIN78MyDplkEgShMCUIlnKVgVAVeIL4pXXY0VzSExsLZPdSZzxjJkfX71D38cItZvMy0YpbKye--NNeT0bh3Tomd12EW1AAdNcOFsjDbbn_pa2ThIa_zYKV1RErGaiqR-uN33LV-JUKm-H6SrWEurQFUU9O-BLvIKrPcdGn_ZP7LhTJSQSzia576nMQtbhwz8k4uk9Tn3scHnFpNNJ-BdlV-VJmxSSTlz9c8vsy4woTK4TB-kkfz47AKxZg0RU8oilcgIikrfo_kO5HCoQwAMqTqxsJhA/https%3A%2F%2Fgithub.com%2Fthomas-vincent%2Fnipic%2Fwiki%2F%255BFreesurfer%255D-Get-surfaces-of-subcortical-structures https://secure-web.cisco.com/1yhlZBs4CaRuE7OrwrGVtEsQL33d47WfL9Yu02tKHEzKqGis-VZ2QsUo3wc0I-F9Xl4CD42o42gUtGEvKCz8usWl7X-3fhwsXAu2DKmngoloe8OIoLcqBvxP7uX_nAUAOzJVhL1v1X1wGpSSCDx2i646Rrxd1R0iGBv28T3TEcEzQA7Mfpl98Tse0ab3SdW04eOZHbRzG0bqADUjE7WXLR3jQUj9GAT4IkULnuGhhv7CP9gF2IIOAaNcBqU8xsijZDxWuelDUPELsRrWlxOJ6HSBWWntUhP7GZF336sA8O4ErBZai7rjk2BwMvCxskkvPYYEduQ_YepFNicYE-rsWnA/https%3A%2F%2Fgithub.com%2Fkhanlab%2Fsurfmorph https://secure-web.cisco.com/1SH8G6D-66tFkOVdkMhKlZU3DoZJWFrankZvFbDjhud520NPLJFMbPVEY3QEkx1Anjs_T-mOZ802DkO8IMAoKICsuHGbfGHzlCBpuLpBo3eG6xOMEBAvyPoDJp4Foco_c278n-AKuUSqWStoiyqybIWHuEDnEVXSCFHtEcCER3WFc7Y05QDcELHJxcVyfuqIM49409LcHzosBJuWF2rTNTteyik5rMYdclhak8oiyez2cmqdIO_JRAajAd0aadfNPhe0A7A41RkGowT8gzaCssM-DEIHPy8MjjNu8X8iL8dp0yAyktpa1nICSQP4S41QtHxJqzOkF7bZHOU6xFerjNA/https%3A%2F%2Fgsl.lab.asu.edu%2Fmtsms%2F inaivu/aseg2srf at master * aestrivex/inaivu * GitHub<https://secure-web.cisco.com/1Dfh65Cci0nD0VovbWbYJTBewgjEMy6UwWY0YW-6fsinPTBp81H87rPKf1gjp5xlDLEHHbIm9Ec53aY78S7yly5w38UYTvhK1VPN-QFUGiMXfVQU4G1Ers5KjZexTRr8YPh6SK8kpeLbEyVH_U8ghvZHLiMlA4gG3u_GCJa9oZDKQzWPd5M5ZkQykz6mwjH75rMkfmzc7uk3g4PaYh9zZbo3zCRs5AigeSE6MLXJQOyp2sw0Keqz7UlYInhbG8KPy0pqV-0bv5xqyi5g_DAMjnVQVPXxYLoKiigwYPRJW7bWWlown9XxdF9UfEjxkVX7B54w0GXU-S27o2npaFWxc-g/https%3A%2F%2Fgithub.com%2Faestrivex%2Finaivu%2Fblob%2Fmaster%2Faseg2srf> The above tools may be able to generate subcortical surfaces, but I would then need to convert them back to freesurfer formats to run mris_anatomical_stats, which I am lost with. If anyone has any advice for this, this would be great! Within freesurfer, I am aware of tools such as mri_vol2surf, as well as other such as mris_sample_parc - Free Surfer Wiki (harvard.edu)<https://secure-web.cisco.com/1zui1UwPJX5g6ACi-dDQWDrdF2r3cGq_2t5-DhB34ZuQ879YX0cW5joYi3MGv0eTCDmGUXBH7f0Y1bXRflQZM8g1vjKxkEsIlj6yUiHybc9M7ACuOclaHX4IQHcLN3NaCq40o5YW-EB3fvN15eDqBspKDj-sECzaFHEGde2bmzIYmOtDK9VETY1O99F61OqXvNW9tG96kk69jkDueGPiRADuik8KuMbSVdFcXXupp9pkkBtyDTotM5BbH53esMaJDeYNUyUdHjUu3A6R-gIt1KsfdZxWaHnn-RrUbmoWSnL3JCeon2dIAPOHpbBXkRx7kMZeHSHizSKCPVSwH5G_E9A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_sample_parc>. I am a bit lost as to how to use these tools, as the documentation is limited, and threads are more looking at generating these surfaces for visualizations rather than anatomical statistics. I am also wondering if there are any additional processing steps, perhaps normalization, that may be required before creating the MSN. If anyone has tried this before or has any advice, I would love to hear. I am relatively new to this area, using freesurfer past recon-all, so any help is appreciated! Many thanks, Sam
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