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Dear Freesurfer developers,
I have a cohort of subjects that are already run under FS 6. I recently upgraded Freesurfer from 6.0 to 7.1.1, and now I also have run these subjects under FS 7.
When comparing the cortical thickness results obtained from FS6 and FS7, I found that FS 7 results are much smaller than the FS6 ones. On average, about 13%-21% decrease in the subject's average cortical thickness. Specifically, on a cohort of images from GE scanners, the average cortical thickness from FS6 is 2.5mm, but from FS7 is less than 2.0mm.
According to some published papers, I think 2.5mm as the average cortical thickness is more accurate than 2.0mm.
Have you encountered this issue or question before? Do you think I should keep using FS6? Please give me your advice. Thank you!
John.
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For what it’s worth, we had problems with FreeSurfer 7.X with surface placement accuracy on HCP-Style data (i.e. 0.8-0.7mm isotropic T1w and T2w) and have continued to recommend using FreeSurfer 6 for the HCP Pipelines for now. We usually quote 2.6mm average cortical thickness for young adults, but it does depend on age.
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Xiaojiang Yang xjyangxj@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, March 12, 2021 at 10:29 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Cortical thickness on version 6 vs 7
External Email - Use Caution Dear Freesurfer developers,
I have a cohort of subjects that are already run under FS 6. I recently upgraded Freesurfer from 6.0 to 7.1.1, and now I also have run these subjects under FS 7.
When comparing the cortical thickness results obtained from FS6 and FS7, I found that FS 7 results are much smaller than the FS6 ones. On average, about 13%-21% decrease in the subject's average cortical thickness. Specifically, on a cohort of images from GE scanners, the average cortical thickness from FS6 is 2.5mm, but from FS7 is less than 2.0mm.
According to some published papers, I think 2.5mm as the average cortical thickness is more accurate than 2.0mm.
Have you encountered this issue or question before? Do you think I should keep using FS6? Please give me your advice. Thank you!
John.
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I have not seen anything of that magnitude. I do see a systematic drop in the thickness with v7 relative to v6, but it is on the order of 1 or 2%. It might be something specific to the pulse sequence that you are using. Try looking at the surfaces of the subject that has the largest discrepancy. You can use fvcompare, eg,
fvcompare --s subjectname --sd1 /path/to/v6/subjectsdir --sd2 /path/to/v7/subjectsdir
This will bring up surfaces and segs from both analysis in one freeview command so that you can inspect them.
On 3/12/2021 11:29 AM, Xiaojiang Yang wrote:
External Email - Use Caution
Dear Freesurfer developers,
I have a cohort of subjects that are already run under FS 6. I recently upgraded Freesurfer from 6.0 to 7.1.1, and now I also have run these subjects under FS 7.
When comparing the cortical thickness results obtained from FS6 and FS7, I found that FS 7 results are much smaller than the FS6 ones. On average, about 13%-21% decrease in the subject's average cortical thickness. Specifically, on a cohort of images from GE scanners, the average cortical thickness from FS6 is 2.5mm, but from FS7 is less than 2.0mm.
According to some published papers, I think 2.5mm as the average cortical thickness is more accurate than 2.0mm.
Have you encountered this issue or question before? Do you think I should keep using FS6? Please give me your advice. Thank you!
John.
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Xiaojiang Yang