Hi All,
I have run recon-all on a subject with a large cortical dysplasia, and while the segmentation (aseg) seems to be relatively correct, there is a large region of dysplasia not included by the pail surface. The normalized intensity values for the cortex and the excluded region are very similar so it seems that there is a threshold related to the distance from the white matter surface to the pial surface, or perhaps normal gyrification that is constraining the pial surface.
Is there a recon-all or expert option for surface reconstruction of abnormally thick cortex?
Thanks in advance, Jonathan
Hi Jonathan
it really depends on the characteristics of the dysplasia. We have some experience with this and in general FS does really well, but if it's a large region of cortex that is 8mm thick things will probably fail. Do you have a highres FLAIR/T2? That can help.
If you upload the subject I'll take a look Bruce
On Sat, 9 Nov 2013, Jonathan DuBois wrote:
Hi All, I have run recon-all on a subject with a large cortical dysplasia, and while the segmentation (aseg) seems to be relatively correct, there is a large region of dysplasia not included by the pail surface. The normalized intensity values for the cortex and the excluded region are very similar so it seems that there is a threshold related to the distance from the white matter surface to the pial surface, or perhaps normal gyrification that is constraining the pial surface. Is there a recon-all or expert option for surface reconstruction of abnormally thick cortex?
Thanks in advance, Jonathan
Hi Bruce,
Thanks for getting back to me. Unfortunately, we don't have a FLAIR/T2 for this subject. In some places the cortex is thicker than 8mm. I attached a couple screenshots. Is there somewhere specific that I can upload the file?
Best, Jonathan
[image: Inline image 4][image: Inline image 3]
On Fri, Nov 15, 2013 at 9:16 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Jonathan
it really depends on the characteristics of the dysplasia. We have some experience with this and in general FS does really well, but if it's a large region of cortex that is 8mm thick things will probably fail. Do you have a highres FLAIR/T2? That can help.
If you upload the subject I'll take a look Bruce
On Sat, 9 Nov 2013, Jonathan DuBois wrote:
Hi All,
I have run recon-all on a subject with a large cortical dysplasia, and while the segmentation (aseg) seems to be relatively correct, there is a large region of dysplasia not included by the pail surface. The normalized intensity values for the cortex and the excluded region are very similar so it seems that there is a threshold related to the distance from the white matter surface to the pial surface, or perhaps normal gyrification that is constraining the pial surface. Is there a recon-all or expert option for surface reconstruction of abnormally thick cortex?
Thanks in advance, Jonathan
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Hi Jonathan
yes, checkout our wiki which lists our upload site. Tar and gzip the subject and put it at: https://gate.nmr.mgh.harvard.edu/filedrop2/
Bruce
On Fri, 15 Nov 2013, Jonathan DuBois wrote:
Hi Bruce, Thanks for getting back to me. Unfortunately, we don't have a FLAIR/T2 for this subject. In some places the cortex is thicker than 8mm. I attached a couple screenshots. Is there somewhere specific that I can upload the file?
Best, Jonathan
Inline image 4 Inline image 3
On Fri, Nov 15, 2013 at 9:16 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Jonathan
it really depends on the characteristics of the dysplasia. We have some experience with this and in general FS does really well, but if it's a large region of cortex that is 8mm thick things will probably fail. Do you have a highres FLAIR/T2? That can help. If you upload the subject I'll take a look Bruce On Sat, 9 Nov 2013, Jonathan DuBois wrote: Hi All, I have run recon-all on a subject with a large cortical dysplasia, and while the segmentation (aseg) seems to be relatively correct, there is a large region of dysplasia not included by the pail surface. The normalized intensity values for the cortex and the excluded region are very similar so it seems that there is a threshold related to the distance from the white matter surface to the pial surface, or perhaps normal gyrification that is constraining the pial surface. Is there a recon-all or expert option for surface reconstruction of abnormally thick cortex? Thanks in advance, JonathanThe 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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