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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

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