Subcortical Surface Based Morphology

Dear community,

I am relatively new to this research area, particularly around surface morphology, so I apologise for any basic errors that I might make.

In my research I am currently looking at the integration of cortical and subcortical features for creating Morphological Similarity Networks (MSNs). I have found a lot of research using MSNs focusing on cortical surface maps, and excluding subcortical regions. I suppose this may be due to the way tools like freesurfer process these (vertex for cortex, and volume for subcortical) separately…
>Is this the main reason why they are often not included? And if not, is this due to fundamental differences in cortical and subcortical areas?

I have my data processed with freesurfer recon-all, and plan to use freesurfer tools to extract features such as thickness, volume, curvature, and surface area. I can currently do this with for the aparc cortical regions, but not for the aseg subcortical regions. I have identified a couple of possible methods and resources which may work:

  1. Extract volumetric features, from both anatomical T1w, and DWI microstructural metrics for cortical and subcortical areas (i.e. VBM).

  2. Convert subcortical regions to surface regions i.e. with vol2surf, but I am unsure if this is suitable for my use case. I have also identified surfmoroph, and mTBM which are external to freesurfer and require further conversion from other filetypes to freesurfer acceptable formats.

  3. Use a separate tool than freesufer that might enable subcortical surface maps internally. ← I am currently unare of any…

  4. Process surface tissue maps, and then segment surface cortical and subcortical regions from this (i.e. like in this work).

>Does anyone have any thoughts about these methods?

Ideally I would like to avoid volume based morphology due to the issues around Partial Volume Correction (PVC), so I would like to avoid solution 1, even though it is the most straightforward. Using tools within freesurfer such as vol2surf would be ideal, but I unsure if this is suitable.

>TLDR: I am wondering if anyone has addressed the issue around including both cortical and subcortical features for MSNs in the past, and may have any advice or further resources to help me move forward? Anything is appreciated!

Many thanks,
Sam :grinning: