Hello,
I developed a new atlas for parcellating the cerebellum, based on 20 brains manually segmented by Jörn Diedrichsen, which he was kind enough to share (note these also formed the basis for his 2009 paper in Neuroimage (46; 39-46).
I got the segmentation to work, but I would not say it works well. As you can see from the attached image, it is not ready for prime-time. On the left is the brain of subject 1, manually segmented. On the right is the brain of the same subject with the automated sementation, based on the developed atlas.
My question is, how can I improve it? I realize this is an open question and potentially difficult to answer without some probing, but this is a resource I think a lot of users would like to have access to, so perhaps it is worth the effort.
Anthony
Hello,
I developed a new atlas for parcellating the cerebellum, based on 20 brains manually segmented by Jörn Diedrichsen, which he was kind enough to share (note these also formed the basis for his 2009 paper in Neuroimage (46; 39-46).
I got the segmentation to work, but I would not say it works well. As you can see from the attached image, it is not ready for prime-time. On the left is the brain of subject 1, manually segmented. On the right is the brain of the same subject with the automated sementation, based on the developed atlas.
My question is, how can I improve it? I realize this is an open question and potentially difficult to answer without some probing, but this is a resource I think a lot of users would like to have access to, so perhaps it is worth the effort.
Anthony
HI Anthony
I would make sure to include an entire brain labeling in the training set. You can do this by pasting your manual labels into our aseg of the subjects in question.
cheers Bruce
On Fri, 20 Apr 2012, Anthony Dick wrote:
Hello,
I developed a new atlas for parcellating the cerebellum, based on 20 brains manually segmented by Jörn Diedrichsen, which he was kind enough to share (note these also formed the basis for his 2009 paper in Neuroimage (46; 39-46).
I got the segmentation to work, but I would not say it works well. As you can see from the attached image, it is not ready for prime-time. On the left is the brain of subject 1, manually segmented. On the right is the brain of the same subject with the automated sementation, based on the developed atlas.
My question is, how can I improve it? I realize this is an open question and potentially difficult to answer without some probing, but this is a resource I think a lot of users would like to have access to, so perhaps it is worth the effort.
Anthony
Thanks Bruce. What's the easiest way to "paste" those labels. Manually through tkmedit, or through the command line?
Anthony
On 4/20/12 3:53 PM, Bruce Fischl wrote:
HI Anthony
I would make sure to include an entire brain labeling in the training set. You can do this by pasting your manual labels into our aseg of the subjects in question.
cheers Bruce
On Fri, 20 Apr 2012, Anthony Dick wrote:
Hello,
I developed a new atlas for parcellating the cerebellum, based on 20 brains manually segmented by Jörn Diedrichsen, which he was kind enough to share (note these also formed the basis for his 2009 paper in Neuroimage (46; 39-46).
I got the segmentation to work, but I would not say it works well. As you can see from the attached image, it is not ready for prime-time. On the left is the brain of subject 1, manually segmented. On the right is the brain of the same subject with the automated sementation, based on the developed atlas.
My question is, how can I improve it? I realize this is an open question and potentially difficult to answer without some probing, but this is a resource I think a lot of users would like to have access to, so perhaps it is worth the effort.
Anthony
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
probably in matlab On Fri, 20 Apr 2012, Anthony Dick wrote:
Thanks Bruce. What's the easiest way to "paste" those labels. Manually through tkmedit, or through the command line?
Anthony
On 4/20/12 3:53 PM, Bruce Fischl wrote:
HI Anthony
I would make sure to include an entire brain labeling in the training set. You can do this by pasting your manual labels into our aseg of the subjects in question.
cheers Bruce
On Fri, 20 Apr 2012, Anthony Dick wrote:
Hello,
I developed a new atlas for parcellating the cerebellum, based on 20 brains manually segmented by Jörn Diedrichsen, which he was kind enough to share (note these also formed the basis for his 2009 paper in Neuroimage (46; 39-46).
I got the segmentation to work, but I would not say it works well. As you can see from the attached image, it is not ready for prime-time. On the left is the brain of subject 1, manually segmented. On the right is the brain of the same subject with the automated sementation, based on the developed atlas.
My question is, how can I improve it? I realize this is an open question and potentially difficult to answer without some probing, but this is a resource I think a lot of users would like to have access to, so perhaps it is worth the effort.
Anthony
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Bruce,
Can you point me somewhere in the right direction? Is there some example I could start with? I don't use Matlab, although it seems similar to R so I should be okay with learning the syntax, but I just need a place to start.
Anthony
On 4/20/12 4:02 PM, Bruce Fischl wrote:
probably in matlab On Fri, 20 Apr 2012, Anthony Dick wrote:
Thanks Bruce. What's the easiest way to "paste" those labels. Manually through tkmedit, or through the command line?
Anthony
On 4/20/12 3:53 PM, Bruce Fischl wrote:
HI Anthony
I would make sure to include an entire brain labeling in the training set. You can do this by pasting your manual labels into our aseg of the subjects in question.
cheers Bruce
On Fri, 20 Apr 2012, Anthony Dick wrote:
Hello,
I developed a new atlas for parcellating the cerebellum, based on 20 brains manually segmented by Jörn Diedrichsen, which he was kind enough to share (note these also formed the basis for his 2009 paper in Neuroimage (46; 39-46).
I got the segmentation to work, but I would not say it works well. As you can see from the attached image, it is not ready for prime-time. On the left is the brain of subject 1, manually segmented. On the right is the brain of the same subject with the automated sementation, based on the developed atlas.
My question is, how can I improve it? I realize this is an open question and potentially difficult to answer without some probing, but this is a resource I think a lot of users would like to have access to, so perhaps it is worth the effort.
Anthony
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Anthony,
in matlab it would be something like:
vaseg = load_mgh('aseg.mgz') ; [vmanual,M,mr] = load_mgh('manual_seg.mgz') ; ind = find(vmanual > 0) ; vaseg(ind) = vmanual(ind) ; save_mgh(vaseg, 'manual_seg.with_aseg.mgz', M, mr) ;
cheers Bruce
On Sun, 22 Apr 2012, Anthony Dick wrote:
Hi Bruce,
Can you point me somewhere in the right direction? Is there some example I could start with? I don't use Matlab, although it seems similar to R so I should be okay with learning the syntax, but I just need a place to start.
Anthony
On 4/20/12 4:02 PM, Bruce Fischl wrote:
probably in matlab On Fri, 20 Apr 2012, Anthony Dick wrote:
Thanks Bruce. What's the easiest way to "paste" those labels. Manually through tkmedit, or through the command line?
Anthony
On 4/20/12 3:53 PM, Bruce Fischl wrote:
HI Anthony
I would make sure to include an entire brain labeling in the training set. You can do this by pasting your manual labels into our aseg of the subjects in question.
cheers Bruce
On Fri, 20 Apr 2012, Anthony Dick wrote:
Hello,
I developed a new atlas for parcellating the cerebellum, based on 20 brains manually segmented by Jörn Diedrichsen, which he was kind enough to share (note these also formed the basis for his 2009 paper in Neuroimage (46; 39-46).
I got the segmentation to work, but I would not say it works well. As you can see from the attached image, it is not ready for prime-time. On the left is the brain of subject 1, manually segmented. On the right is the brain of the same subject with the automated sementation, based on the developed atlas.
My question is, how can I improve it? I realize this is an open question and potentially difficult to answer without some probing, but this is a resource I think a lot of users would like to have access to, so perhaps it is worth the effort.
Anthony
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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