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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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.
- 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?
- 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.
- 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
Messenger°²È«±£»¤ÖÐÐÄ£¬Ãâ·ÑÐÞ¸´ÏµÍ³Â©¶´£¬±£»¤Messenger°²È«£¡ http://im.live.cn/safe/
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.
- 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?
- 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.
- 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
Messenger°²È«±£»¤ÖÐÐÄ£¬Ãâ·ÑÐÞ¸´ÏµÍ³Â©¶´£¬±£»¤Messenger°²È«£¡ http://im.live.cn/safe/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: nicks@nmr.mgh.harvard.edu To: fischl@nmr.mgh.harvard.edu CC: caoaize@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.
- 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?
- 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.
- 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
Messenger°²È«±£»¤ÖÐÐÄ£¬Ãâ·ÑÐÞ¸´ÏµÍ³Â©¶´£¬±£»¤Messenger°²È«£¡ http://im.live.cn/safe/
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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: nicks@nmr.mgh.harvard.edu To: fischl@nmr.mgh.harvard.edu CC: caoaize@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.
- 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?
- 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.
- 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
Messenger°²È«±£»¤ÖÐÐÄ£¬Ãâ·ÑÐÞ¸´ÏµÍ³Â©¶´£¬±£»¤Messenger°²È«£¡ http://im.live.cn/safe/
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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: fischl@nmr.mgh.harvard.edu To: caoaize@hotmail.com CC: nicks@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: nicks@nmr.mgh.harvard.edu To: fischl@nmr.mgh.harvard.edu CC: caoaize@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.
- 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?
- 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.
- 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
Messenger°²È«±£»¤ÖÐÐÄ£¬Ãâ·ÑÐÞ¸´ÏµÍ³Â©¶´£¬±£»¤Messenger°²È«£¡ http://im.live.cn/safe/
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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: fischl@nmr.mgh.harvard.edu To: caoaize@hotmail.com CC: nicks@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: nicks@nmr.mgh.harvard.edu To: fischl@nmr.mgh.harvard.edu CC: caoaize@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.
- 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?
- 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.
- 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
Messenger°²È«±£»¤ÖÐÐÄ£¬Ãâ·ÑÐÞ¸´ÏµÍ³Â©¶´£¬±£»¤Messenger°²È«£¡ http://im.live.cn/safe/
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freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
caoaize -
Nick Schmansky