In theory it is possible, though I don't know if it is better or worse.
You can run samseg, then run samseg2recon (this creates a folder that
looks like it was created by recon-all), then run subfields on that folder
On 5/5/2020 10:45 AM, Sneha Pandya wrote:
External Email - Use Caution
Dear experts,
I want to revisit if anyone has ran subfield analysis just by running
samseg? If it is possible is it as reliable as from running regular
routine with “-all” recon-all flag?
Thank you,
Sneha
*From:* Sneha Pandya
*Sent:* Thursday, April 30, 2020 4:15 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* samseg with subfields
Dear experts,
Is it possible to run subfield analysis (hippcampal subfields,
amygdalar, thalamic nuclei, and brainstem structures) when we only run
samseg on our dataset?
Thank you,
Sneha
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