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Thanks. I am asking Neuromorphometrics to see if they are willing to give the detailed information. 

In fact, I am comparing Freesurfer with vol2Brain. However, they are using the Neuromorphometrics protocol and thus didn't run this comparison in their original paper. Therefore, I don't know how much of a systematic error I would expect if I do this. I am mostly interested in the ICV, and volumes of white matter, grey matter and subcortical structures. Therefore, I wonder if the protocol difference only occurs in more subtle structures or universal across all structures.

On Tue, Aug 30, 2022 at 2:37 PM Fischl, Bruce <BFISCHL@mgh.harvard.edu> wrote:

Yes, that can definitely be the case. Some boundaries are not visible (in e.g. the accumbens) and so the border is defined by geometric means. Other times the definition of what is in or not in a structure can change (e.g. is the fimbria part of the hippocampal label?)

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ruifeng Dong
Sent: Tuesday, August 30, 2022 2:34 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Segmentation protocol used by Freesurfer

 

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Thanks, Bruce.

 

Actually, I am comparing the volume computations between different segmentation tools. In some software's paper, they mentioned there is a slight difference in protocol from Freesurfer and thus not easy to compare. I am wondering what the difference lies in, for example, in the way a structure is defined anatomically, or something else? 

 

I am new to this field, and don't know if my question is clear to you.

 

Thanks again.

 

On Tue, Aug 30, 2022 at 1:29 PM Fischl, Bruce <BFISCHL@mgh.harvard.edu> wrote:

Hi Ruifeng

 

I think they are similar, but you would have to ask Neuromorphometrics about the differences. Our protocol was published in the Neuron 2002 paper and the papers it cites, which I think is also where the Neuromorphometrics’ protocol came from

 

Cheers

Bruce

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ruifeng Dong
Sent: Tuesday, August 30, 2022 11:07 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Segmentation protocol used by Freesurfer

 

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Is Freesurfer using Neuromorphometrics’ General Segmentation Protocol, or something different?

 

What are the differences between different protocols?

 

Thanks!

 

Ruifeng

 

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