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Hi Douglas,

Thank you for your reply. The regions I am primarily interested in are the segmentations of the Hippocampus and Amygdala, as well as eTIV as a covariate. However, I will also run exploratory analyses on the whole brain, as the study is a clinical group comparison.

Regarding some numbers, please see attached (and in the .zip):

roi_proportional_changes: for each ROI (whole brain) I ran the formula mean(abs((v8 - v7) / v7) to determine the average absolute proportional difference between the versions, which is where I got the ~ 1-200% differences between versions in different ROIs
etiv_differences: this is the eTIV (estimated total intracranial volume) for each participant in my study directly taken from the output of each version of FreeSurfer
amyg_differences: this is an example of an amygdala subfield (Medial Nucleus LH) for each participant in my study directly taken from the output of each version of FreeSurfer

If you could please kindly explain a bit more about why there are big differences between v7 and v8 that would be very helpful, as I am currently not sure which version to move forward with, as the findings are completely different. I was under the impression that v8 is meant to be better, particularly for segmentation, however I am worried about publishing and reviewers, particularly if the outcomes cannot be compared to earlier versions and therefore the current literature.

Thank you again for your help and response.

Kindest,

Hana

From: Douglas N. Greve <dgreve@mgh.harvard.edu>
Date: Monday, 11 August 2025 at 8:36 am
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs

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Please be (much) more specific. What are the regions that you are finding changes in? Can you provide some numbers? There are big differences between v8 and v7 so it does not totally surprise me.

On 8/7/2025 1:40 AM, Hana McMahon wrote:

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Hi,

I’ve processed the same set of T1‐weighted scans with both FreeSurfer v7.2.0 and the newer v8.0.0. When I compare the regional stats (aseg + subfield tables), the absolute proportional differences are surprisingly large (anywhere from ~1 % up to nearly 200 %, depending on the structure).

I first noticed the issue while running ANCOVAs: with the v8 outputs, estimated total intracranial volume (eTIV) is highly significant in every model, whereas the v7 results (using identical R code and covariates) show a very different pattern.

I am wondering:

Are these version‐to‐version shifts expected, given the changes in v8?

Have others reported similar magnitude differences, particularly for eTIV and subcortical/hippocampal measures?

Are large shifts expected from run-to-run as well?

Any insight would be greatly appreciated, as I am concerned by the magnitude of the differences I am seeing between versions, which are significantly changing my results.

Thanks for your time.

Kindest,

Hana

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