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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
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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:
External Email - Use Caution
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*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1sx8Hr4dZUk3aBnYszhx34iVsQLT7VGVWTc88zPGyV7rJT6...
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Sorry for the slow response. 1.1: the results are bound to be different (since they are different methods) but they should be very highly correlated. For the eTIV, please take a look at Figure 4 of https://secure-web.cisco.com/1pF9TRM2P6hqsAScfzof5e0z8hsMO6EE1AbG_H4lgFdrWqt... 1.2: Doug is totally right, about the zeroing of the ERC vs not. We are looking into this…
2. As of today, you’d have to run SynthSR (which is part of recon-all-clinical) and then process this fake 1mm T1 as if it was a new scan. More seamless integration of Synth tools and subregion segmentation is on the to-do list but not there yet.
Cheers,
/Eugenio
-- Juan Eugenio Iglesias http://secure-web.cisco.com/1E89A-F8PBNW1olFMmiK25cpajXkwzWDj9tSwSoYI3-B2X4a...
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Date: Thursday, July 20, 2023 at 4:30 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu, Gopinath, Karthik KGOPINATH@mgh.harvard.edu Subject: Re: [Freesurfer] Questions for the estimated brain volume based on new version of FreeSurfer
External Email - Use Caution 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:
External Email - Use Caution 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.lmstar11@gmail.commailto:ken.lmstar11@gmail.com
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