Hi Aize,
I think hippocampus will probably be the hardest since it shares so much
of a border with dark things that will be low contrast in your images. I
didn't really look at other structures - did they appear accurate? One
thing you can try is to manually correct a single image, then there are
some switches I can dig up that will take the intensity distribution
parameters from it instead of from the atlas, that should help.
cheers
Bruce
On Tue, 18 Aug 2009, caoaize wrote:
Hi, Bruce,
Do you mean that we can not use freesurfer for hippocampus volume segmentation,
if my data are with the same scanning parameters? We did statitical analysis
for volumes of other sub-cortical areas from freesurfer, found some interesting
results. If you said that the gray matter is too dark in our image, can we
still use it for other sub-cortical areas volume segmentation?
I will be appreciated for your answer.
With my best regards,
Aize
Date: Mon, 17 Aug 2009 17:01:40 -0400
From: fis...@nmr.mgh.harvard.edu
To: caoa...@hotmail.com
CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] (no subject)
Hi Aize,
I think the hippocampal gray matter is so dark in your images that it is
very difficult to distinguish from CSF. Do you have a lot of data collected
with these parameters? If not, we probably could suggest some better ones.
cheers,
Bruce
On Tue, 18 Aug 2009, caoaize
wrote:
Hello Bruce,
The sequence we used is called Turbo field Echo, I need to check it again.
I checked our scanning protocol, found that we did have marker on the subjects'
forehead. I generate the right hippocampus from freesurfer, overlay with
orig.nii (from orig.mgz), the overlay shows that the subject's right side is
the right side in freesurfer's statistical report. It means that our left side
is bigger than the right side. This result consitently appears on our other
subjects data.
I extract the hippocampus left side mask in this way:
mri_binarize --i aseg.mgz --match 17 --o hippo_left.nii
The label for right side is 53. Anything wrong for what I used?
Also, I used asegstats2table --subject s1 s2... --meas volume --tablefile
stats.txt to get the statistical report.
If we accept the low corelation between manual and auto segmentation, how can
we explain that the left side is bigger than the right side?
I hope your help. Thanks a lot.
Best Regards,
Aize
Date: Mon, 17 Aug 2009 13:51:26 -0400
From: fis...@nmr.mgh.harvard.edu
To: caoa...@hotmail.com
Subject: RE: [Freesurfer] (no subject)
wow, I don't think I've ever seen a T1-weighted MR with gray matter this
dark. The gray/csf contrast is very low. What kind of sequence is it?
On Tue, 18 Aug 2009, caoaize wrote:
Hi, Bruce,
Here is the aseg.mgz and norm.mgz files. Thanks.
Aize
Date: Mon, 17 Aug 2009 13:27:07 -0400
From: fis...@nmr.mgh.harvard.edu
To: caoa...@hotmail.com
Subject: RE: [Freesurfer] (no subject)
Hi Aize,
I need the aseg.mgz as well (and probably the norm.mgz). Differences in
the definitions of what is hippocampus and what isn't will reduce the
correlation coefficient. They should still be somewhat correlated, but even
a perfect pair of segmentations under each protocol for each subject will
not have a perfect correlation, so it's hard to assess what it means, since
the protocols are different.
Bruce
On Tue, 18 Aug 2009, caoaize wrote:
Our data is 3T, the manual segmentation follow the McConnell protocol described in
"Volumetry of hippocampus and amygdala with high-resolution MRI and
three-dimensional analysis software: minimizing the discrpancies between
laboratories". I do not know what is the difference between yours and theirs. But,
if both method are consistant, then the correlation coeffienct should be high. Here is
one image that has bad segmention on happocampus.
I am appreciate for your help.
Aize
Date: Mon, 17 Aug 2009 11:52:19 -0400
From: fis...@nmr.mgh.harvard.edu
To: caoa...@hotmail.com
CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] (no subject)
it lost interior voxels? That doesn't sound right. Can you send us an
image? If your manual protocol is different than the one we used then the
DICE overlap is somewhat irrelevant.
cheers,
Bruce
On Mon, 17 Aug 2009, caoaize wrote:
Hi, Bruce,
I am not clear what manual segmentation protocol we are using, it was done by a
trained RA. Currently we just calculate the volumes correlation between manual
segmentation and the auto one, but not your DICE method. Our aquisitions are:
Philips 3D sense, T1TFE, TR 7.9ms.
In 27 subjects, we have two hippocampus volumes from Freesurfer auto
segmentation around 1700, it keeps the edge, but lost lots of inside voxels. I
am thinking to manual edit these two volumes, but do not know what happened.
Aize
Date: Sat, 15 Aug 2009 09:14:30 -0400
From: fis...@nmr.mgh.harvard.edu
To: caoa...@hotmail.com
CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] (no subject)
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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