Yes, I created my own atlas for use with 1-2 year olds. It seems to be happening for all of the subjects. I am wondering if changing the recon-all code to load the manual talairach.lta file for the EM_registration and CA_normalization would possibly fix the problem. It seems strange that the wm/gm means were OK for skull stripping, but then suddenly null for the other steps.
On Mon, May 12, 2014 at 7:49 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Mark > > did you create your own .gca file? If so, why? Does it happen for all your > subjects? > Bruce > > > > > > On Mon, 12 May 2014, Mark Plantz wrote: > > As a quick update to this problem, it looks like the wm_mean and gm_mean >> are reasonable >> during the #SkullLTA and #SkullStripping steps. However, wm mean = 0 and >> gm mean = 0 for the >> #CA_normalize and #EM_registration steps. >> Could this have anything to do with using a manual talairach alignment in >> previous steps? I >> did include the -nogcareg flag with the recon-all command. >> >> >> On Mon, May 12, 2014 at 4:36 PM, Mark Plantz <markplantz2016@u. >> northwestern.edu> wrote: >> Hi Freesurfers, >> Does anyone know if it is possible to manually set the brain centroid >> during the EM >> Registration step of the recon-all pipeline. I am using a non-default >> atlas, and have >> discovered that many of my difficulties have resulted from the brain >> centroid being >> incorrectly assigned to a region of black space. Thank you for the help! >> >> Best, >> >> MP >> >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > 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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