[Freesurfer] How do we account for different scanner/acquisition parameters in the FreeSurfer longitudinal pipeline?

10 seconds ... *** Thank you Sincerely, 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...

[Freesurfer] Comparison of "segment_subregions" and "recon-all"

External Email - Use Caution Hi Iglesias, Okay. I got it. Thank you for informing me. I will try it. Sincerely, Yoonho -- *Hwang, Yoonho* *Research professor* *Institute of Human Genomic Study,* *College of Medicine, Korea University* *#123, Jeokgeum-ro, Danwon-gu, Ansan-si

[Freesurfer] Comparison of "segment_subregions" and "recon-all"

us, brainstem) using "asegstats2table" and the total volume (hippocampus, amygdala, thalamus, brainstem) using "segment_subregions". Is there a standard for how much difference is acceptable? Thank you very much Sincerely, Yoonho -- *Hwang, Yoonho* *Research professor* *Institute of Hu

[Freesurfer] Questions about FreeSurfer's longitudinal pipeline prior to longitudinal analysis

512 x 180) 1st follow-up (scanner1, 512 x 512 x 180) 2nd follow-up (scanner2, 448 x 448 x 192 or 448 x 448 x 208) Could I ignore the warning? Or is there anything I need to fix before running the long)? Also, could you please give me any suggestions on longitudinal analyses? Thank you very m

[Freesurfer] Issues for longitudinal pipeline-based process

External Email - Use Caution Dear FreeSurfer developers, Hi, Prior to the FreeSurfer-based longitudinal analysis, it's inevitable that the scanner will change over time in a long follow-up study. We had multiple follow-up data for the same subjects [e.g., baseline and 1st follow-

[Freesurfer] over-estimated brain volume based on (recon-all / recon-all-clinical) ?

stand. 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...@gmai

[Freesurfer] Questions for the estimated brain volume based on new version of FreeSurfer

stand. 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...@gmai

[Freesurfer] Additional question in "SynthSR and SynthSeg" FreeSurfer list - RE. 2022.12.15

R and SynthSeg? And then, can you tell me what I need to do to measure the brain morphological property (e.g., cortical thickness and volume, etc) after using synthSR and synthSeg? Thank you very much. Best regards, Yoonho -- *Hwang, Yoonho* *Research professor* *Institute of Human Genomic

[Freesurfer] SynthSR and SynthSeg

External Email - Use Caution 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 SynthS

[Freesurfer] Questions for FreeSurfer 7.3.2 recon-all process INCLUDING SynthSeg

reeSurfer 7.3.2. (In other words, can we simply proceed with the recon-all process?)* 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 -- *Hwang, Yoonho*

[Freesurfer] Shortening recon-all process time and longitudinal process

External Email - Use Caution Dear Bruce Fischl, Hi, I'm Yoonho. In the previous post, "Re:[Freesurfer] Inquiry about process time by use "recon-all" (Fri, 12 Jan 2018 12:29:19-0800)", I found that the process time for recon-all depend on both how abnormal the anatomy is and how hi

[Freesurfer] Some func. error during recon-all process

g: see attached Thank you very much. Sincerely, Yoonho -- *Hwang, Yoonho* *Medical Image Processing Laboratory (MIPL),* *Department of Biomedical Engineering, Yonsei University.* *#218 Sanhak-Kwan, 1, Yeonsedae-gil, Heungeop-myeon, Wonju,* *Gangwon-do, 26493, Republic of Korea.* *Office:

[Freesurfer] Curvature Stats func. error among step by step in recon-all process

8~18.04.1-Ubuntu SMP Sat Mar 20 14:10:07 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank you very much. Sincerely, Yoonho -- *Hwang, Yoonho* *Medical Image Processing Laboratory (MIPL),* *Department of Biomedical Engineering, Yonsei University.* *#218 Sanhak-Kwan, 1

[Freesurfer] MCSRCH error using sample data (001.mgz and 002.mgz)

ion: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 2) Platform: Ubuntu release 18.04.1 3) uname -a: Linux LABPC 5.4.0-70-generic #78~18.04.1-Ubuntu SMP Sat Mar 20 14:10:07 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank you very much. Sincerely, Yoonho --