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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:
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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).
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