On 12/15/2022 2:00 AM, Yoonho Hwang wrote:
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Dear FS developers,
Hi, I'm Yoonho. I know that new features, such as SynthSeg, SynthStrip, segment_subfields (beta version), etc, based on deep learning have been added after the FreeSurfer 7.3.2. Here I have questions (I read papers related to SynthSR, SynthSeg, SynthStrip, segment_subfields).
*1. Can I use the SynthSR functions o**nly by FreeSurfer development (dev) version (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ https://secure-web.cisco.com/1ps3QL5XW2qOOptSgD9TqOIsWnQJlFGcz9nxZ59lvSiCbI0zAyu9rH494zDXoBNb27gg8wc3mz4Qz8TYV3WW5NPN9nFsTL-FDMbvhZXIjaWp4l6sfUKU_JwXBnSSafegfW3eIiHFruSaXD7Ruhis6SbHMMQGHC6FkqmJnEEQffGvtfNm5yUFzAyQEKRaZcFvw2vpJjdT_j26w0wJr_ihH8bLl9_vXjsOwQlEax5KS6HoOLF1IpKt4TSoqwnUEfDGxOdjiHVbsyLQA3IW2qHa_r8SpCNsc0kKaj6pyKreB1SfG45KHxzpj5q2xEDDopOe9ZfXqLnIjDuBByRdCGZJ1vw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F)**?*
It is available in 7.3.2, but it might not be the most recent version
*2. When T1WI data are processed with recon-all, are SynthSR and SynthSeg functions included in the "recon-all" process pipeline? If not, are SynthSR and SynthSeg processed separately?*
*recon-all does not use synthseg or synthsr. you have to run them separately. We are working on getting it embedded.*
*3. Is the recon-all process included in SynthSeg and SynthStrip by default?*
*No*
*4. When I process T1WI data with Freesurfer dev version, is it installed based on the new version in HPC per version update for freesurfer?*
*I don't know what you mean. hcp=?*
** *5. I think using SynthSR and SynthSeg functions can solve the Harmonization issue (data acquired from other manufacturers (Siemens, GE, Philips), protocols (FSPGR, MPRAGE, etc), and other sites). What do you think about that?*
*Not sure. *
*6. In lh.w-g.pct.stats file, I know that "Mean" means GWC (gray/white matter contrast), which is (100/0.5)*[(white matter intensity - gray matter intensity)/(white matter intensity + gray matter intensity)], as far as I know, I want to know in detail whether the 0.5 term should be omitted and 100 is to appear as a percentage.*
*The 0.5 is for computing the mean intensity to it is a percentage relative to the mean*
Thank you for reading my long question Please let me know if there is anything you don't understand. Looking forward to your feedback. Thank you very much.
Sincerely, Yoonho
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