The command is defect-seg doug On 02/11/2013 03:09 PM, Kristina Nalbandian wrote: > 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] <mailto:[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 list >> [email protected] <mailto:[email protected]> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > [email protected] <mailto:[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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