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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?
- 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.*
*Email: ken.lmstar11@gmail.com*
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