Hi Aize,
you are using the CMA manual segmentation protocol? We have not found a
bias in volumes, and our DICE is usually close to .9 for hippocampus.
What acquisitions are you using?
cheers,
Bruce
On Sat, 15 Aug 2009, caoaize wrote:
Hi, Bruce,
Our segmentation protocol is the same one as Freesurfer's auto segmentation, I
used recon-all -s subject -all, command. I do not know in this protocol,
whether fimbria and alveus are included. We do not have skin fiducial to tell
right or left side. The interesting thing the mean volume for auto is less than
manual segmentation.
Aize
Subject: Re: [Freesurfer] (no subject)
From: ni...@nmr.mgh.harvard.edu
To: fis...@nmr.mgh.harvard.edu
CC: caoa...@hotmail.com; freesurfer@nmr.mgh.harvard.edu
Date: Fri, 14 Aug 2009 18:53:41 -0400
just to add a factoid, from the ADNI data set, 793 subjects processed by
freesurfer:
Volume Mean: StdDev:
------------------- ----- -------
Left-Hippocampus 3184.335 604.930
Right-Hippocampus 3233.753 621.896
seems pretty symmetric, with the right being slightly larger (but within
std). this subject set is a mix of controls, MCI and AD patients.
n.
On Fri, 2009-08-14 at 17:53 -0400, Bruce Fischl wrote:
is your segmentation protocol the same as the one we base our automated
segmentation on? For example, are fimbria and alveus considered part of
the hippocampus?
As far as left/right switches go, do you have any fiducial markers (e.g.
vitamin E tablets) in the images?
cheers
Bruce
On Sat, 15 Aug 2009, caoaize wrote:
Hi, there,
I have some problem for the hippocampus segmentation results.
1. My structural data are originally in par-rec file. I used r2agui to
convert them into .nii format, then use recon-all -i to convert the .nii
data into freesurfer .mgz format. Based on these operations, I run
recon-all -all on all my data, the statistical report show that the mean
left hippocampus volume is bigger than the right one, while literature
shows that the right one should be bigger. This problem continuously
appeared in our different studies. I am not sure whether it is r2agui's
problem, which changed the oritation of the structural data. Do you have
any idea?
2. After autosegmentation, we did a statistical comparison analysis
between automatic segmentation and manual segmentation, and the
correlation is quite low, less than 80%, which is not acceptable for us.
3. Can I edit the auto segmentation results in Freesurfer if we think the
auto segmentation is not good enough in some area?
I will be really appreciated for your help.
Aize
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