Regarding the Use of Custom atlases containing deep brain nuclei in recon-all segmentation - Freesurfer

12 Apr 2023


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Dear Freesurfers,
I am a neuroscience master's student and new to free surfer. I had a task
of segmenting deep brain nuclei from T1 scans using free surfer, which I
was able to do successfully, but ran into some problems. The atlas used by
Freesurfer for the segmentation is the Taiairach atlas, which
doesn't contain the "Subthalamic nucleus" which is an ROI that I require.
Hence I went thoroughly through the mailing list/ free surfer documentation
about how I can implement a custom atlas containing subcortical structures
( that is *in.nii format* and has a *CSV file* for the regions in the
atlas) in the recon-all function, but I wasn't able to gather any concrete
information about how to do so. Hence, I have a kind request as to whether
someone can spare me a bit of their precious time and send me a
step-by-step guide from their experience with the same problem.
Thank you for your time! :) ,
Warm regards
Abhishek