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_BvEcAItpkOmdAs3fMgTWn1abKwPfBB... https://secure-web.cisco.com/1u1Ru_EifdWYQsjg7F-GHFGBp-Vkvjk_3iHSqwgV0CTWKwS... https://secure-web.cisco.com/1yhlZBs4CaRuE7OrwrGVtEsQL33d47WfL9Yu02tKHEzKqGi... https://secure-web.cisco.com/1SH8G6D-66tFkOVdkMhKlZU3DoZJWFrankZvFbDjhud520N... inaivu/aseg2srf at master * aestrivex/inaivu * GitHubhttps://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