Hi Carolina,
the yellow line represents the gray/white boundary, and so presumably should follow the bottom of the heterotopia. If it is large though, it may be difficult to obtain an accurate boundary since it breaks many of our assumptions (e.g. max thickness, sharp intensity gradient at gray/white border, ....)
cheers, Bruce
On Tue, 26 Jul 2011, Carolina Valencia wrote:
Hi Bruce, Yes, it should be classified as a gray matter, if I save a point of an heterotopia in the tkmedit and then open it in tksurfer the point showed at the inflated surface correspond to that point or to the projection of the heterotopia in the cortical surface? what happen with these measures if sometimes the heterotopias are outlined by the yellow line and sometimes are not? I don't know if I'm totally clear.
Thanks,
Best,
Carolina
2011/7/21 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Carolina,
no, the aseg cortex/wm is not used for thickness or volume (it can be, but we don't recommend it). The surfaces are. As for the heterotopias, I don't really know what a good output would be. It depends what you want to do with them. I guess they should be gray matter, no? BruceOn Thu, 21 Jul 2011, Carolina Valencia wrote:
Hi Bruce,thanks for your explanation. I was thinking the the segmentation region is used to calculate cortical thickness, by the way, is it used for calculate something? such as the GM volumes? I want to know this to be sure if in some point I have to fix this. About the heterotopias, is a good output to have someones classified as WM, other as GM and sometimes are outlined by the yellow line and sometimes are not? Best regards, Carolina 2011/7/19 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Carolina, it looks mostly to me like the surfaces are in the right place (the yellow and red lines). Don't look at the colored overlay - that is the aseg voxel segmentation and not what we typically use for cortical morphometry. Only look at the yellow and red lines. cheers Bruce On Tue, 19 Jul 2011, Carolina Valencia wrote: tiff I guess, I took the pictures from FS 2011/7/19 Bruce Fischl <fischl@nmr.mgh.harvard.edu> what format are the files in the archive in? They don't have an extension On Tue, 19 Jul 2011, Carolina Valencia wrote: I hope this attachement works.I also noticed that some heterotopias are classified as WM, other as GM and sometimes are outlined by the yellow line and sometimes are not. Best regards, Carolina 2011/7/19 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Carolina, can you gzip it or use compression? Usually people can send a few images to the list. cheers Bruce On Tue, 19 Jul 2011, Carolina Valencia wrote: Dear FS experts, I'm trying to analyse a case of cortical dysplasia, but after recon-all I see some errors in tkmedit that I don't know what to edit. I found some errors in cortical and subcortical segmentation, I don't find in the failure mode presentation a way to solve this. I saw the pial surface (yellow line) with acceptable accuracy but the GM (the red one) in some regions are misplaced (WM classified as GM and some GM not classified (empty color)) I tried to attached an image to illustrate the problem but I don't succeed, because the mailing list reject my email. How I can send you an image of ~700kb? Thanks a lot, Carolina 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.