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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.*
*
*
*Email: ken.lmsta...@gmail.com*
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