It really can be anything. Hard to say
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Ruifeng Dong
Sent: Tuesday, August 30, 2022 3:01 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Segmentation protocol used by Freesurfer
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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
<bfis...@mgh.harvard.edu<mailto:bfis...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Segmentation protocol used by Freesurfer
External Email - Use Caution
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
<bfis...@mgh.harvard.edu<mailto:bfis...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Segmentation protocol used by Freesurfer
External Email - Use Caution
Is Freesurfer using Neuromorphometrics’ General Segmentation Protocol, or
something different?
What are the differences between different protocols?
Thanks!
Ruifeng
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