Dear Eugenio,

Many thanks for your prompt reply and explanation. May I ask few follow-up questions, please?

1) You mentioned "we rebuilt the atlas ... change the code...", would you please explain a little bit more about what you mean with "rebuilt"? In the FS dev, does the "rebuilt" mean that you use different segmentation algorithm on the same FS v.6.0 ex-vivo atlas template, or even the ex-vivo atlas template per se is already different in FS dev from that in FS v.6.0?

2) Related to 1), given the volume discrepancy between the two FS versions, from your perspective, would you say the current hippocampal subfield segmentation in FS dev is more accurate compared with FS v.6.0 algorithm? Does this further HBT segmentation within subfields help us understand distinct subfield functions along the anterior-posterior axis?

3) In our analyses in patients with atrophy, we noticed that the results between FS dev. and FS v.6.0 were relatively more consistent for patients with less severe atrophy, but inconsistent for patients with more severe atrophy. In your opinion, would you suggest that we use the FS dev to segment the hippocampus in patients with atrophy, or stay with the stable FS v.6.0 version at this moment, since those subfields are already small?

4) For the latest FS dev version, may I know whether you have any plans to further consolidate/optimize the algorithm, or it can be considered as the stable version?

Apologize for so many questions, but I am really interested in this method and find it very helpful.Greatly appreciate your help and reply in advance!

Best,

Liwen

On Monday, 23 September 2019, 8:04:13 pm GMT+8, Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

Dear Liwen,

We rebuilt the atlas and there were also minor changes in the code, so the volume won’t be exactly the same.

Having said that, if you plot 6 vs dev volumes, they should be highly correlated.

Cheers,

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Liwen Zhang <lw.zhang@yahoo.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, 22 September 2019 at 10:40
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] help! Hippocampal subfield segmentation with FS development version

External Email - Use Caution

Hello freesurfer experts,

I previously applied hippocampal subfield segmentation using FS v.6.0. I am now trying to devide subfields into head/body where applicable using FS development version (latest version). However, I encountered the following problems/quesetions:

1) X represents certain subfield (volume)

X_head + X_body (from FS dev) ~= X (from FS v.6.0)

What possibly causes this volume discrepancy between FS dev and FS v.6.0? Is the head/body segmentation template in FS dev based on the same ex-vivo template as used in FS v.6.0?

2) Related to 1), subfield volume as obtained from FS v.6.0 generally larger than that from FS dev (not for all subfields though)

I processed T1 images with FS v.6.0 and then applied hippocampal segmentation with both FS v.6.0 and FS dev.

Any suggestions/comments would be greatly appreicated!

Thank you for your time and help in advance!

Best,

Liwen

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