Thank you for the reply! What is the command for running defect-seg? Will this only help me visualize the defects or will it correct them as well?
Many thanks On Fri, Feb 8, 2013 at 3:25 PM, Douglas Greve <[email protected]>wrote: > Kristina, you can also run defect-seg to create aseg segmentation of the > defects. Follow the instructions in the --help to visualize. Look in that > region for defects. > doug > > > > On 2/8/13 5:56 PM, Bruce Fischl wrote: > > Hi Kristina > > I would guess you have a topological defect that is being fixed > incorrectly. If you upload the subject I'm happy to take a look (in between > rounds of shoveling) > > Bruce > On Fri, 8 Feb 2013, Kristina Nalbandian wrote: > > Hello, > I am trying to run cortical thickness on a few scans. After the > initial > recon-all -all command not all regions of grey and white matter were > included. I have attached a picture of the problem (the right side > temporal > lobe is not included, but the the left side is). I tried adding control > points and re-running the process with the command "-autorecon-all > -autorecon2-cp -autorecon3 -subjid subject name" but I do not get a very > improved result. If there anything else I can try? > > Thank you for all your help, > Kristina Nalbandyan > Neuroscience Undergraduate Interdepartmental Program, UCLA > > > > _______________________________________________ > Freesurfer mailing > [email protected]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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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