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First of all, you are not going to get the same answer from these different programs. For ento, recon-all will zero the thickness in some areas around ento, and clinical is probably not doing that. Still a factor of 4 seems pretty large. Maybe Karthik has looked at it.

On 7/6/2023 11:21 PM, Yoonho Hwang wrote:

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Dear FS developers,

Hi,

I am very happy that we can use new features of FreeSurfer (e.g., recon-all-clinical.sh, SynthSeg, SynthSR, etc.)
While using a variety of functions from FreeSurfer (v7.3.2 and v7.4.1), we would like to hear the answers to the following questions.

1-1. Compared to the recon-all stream, using SynthSeg seems to overestimate the volume in many subregions of the brain including eTIV? Can you explain why this happens?
1-2. The estimated volume of the entorhinal cortex is different between recon-all/SynthSeg and recon-all-clinical.sh. There is a 3-4 times difference. Can you tell me why the result is?

2. Can the functions (segment_subregions, segmentThalamicNuclei.sh, segmentBA.sh, segmentHA.sh, etc.) used in recon-all be used in recon-all-clinical.sh?

Please let me know if there is anything you don't understand.
Looking forward to your feedback.
Thank you very much.    

Best,
Yoonho

--
Hwang, Yoonho
Research professor
Institute of Human Genomic Study,
College of Medicine, Korea University

#123, Jeokgeum-ro, Danwon-gu, Ansan-si, Gyeonggi-do, 15355, Republic of Korea.


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