Hey Bruce. I've sent one of my subjects in which I noticed the segmentation problems in the occipital lobe. Sagittal slice 115 provides a good example. I've also noticed that with my subjects I frequently have problems with segmentation of the temporal lobes, although adding control points usually fixes this quite well.
Thanks for your help Matt On Mon, Jul 28, 2014 at 3:22 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Matt > > there are instructions on our wiki. You can either ftp or use the > filedrop, although ftp is probably best if you are uploading an entire > subject > > > cheers > Bruce > On Mon, 28 Jul 2014, Walton, Matt wrote: > > Hey Bruce. >> Thanks for the response. How do I go about uploading the subject? >> >> On Monday, July 28, 2014, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Matt >> >> certainly something is wrong, but it's hard to tell why from the >> single slice. You have big topological defects that are being >> fixed incorrectly. Can you upload the subject and we will take a >> look? >> cheers >> Bruce >> On Mon, 28 Jul 2014, Walton, Matt wrote: >> >> Hello Freesurfer team, >> I've used freesurfer to segment (recon-all) >> approximately 30 different >> subjects from a study. I've noticed that a large >> number of these subjects >> have a misclassification of the white and pial >> boundaries in the occipital >> lobe (such that grey matter is being classified as >> white matter). I believe >> this problem is originating from my scanner and >> original data. I'm acquiring >> a T1W BRAVO sequence on a GE Discovery 750w 3T >> scanner, using a 32 channel >> phased array head coil. For many subjects, this >> acquistion gives intensity >> inhomogeneity in the occipital lobe. I've begun >> using a GE based correction >> technique (PURE) on the images, and it appears to >> improve the intensity in >> the occipital lobe, but Freesurfer is still >> frequently misclassifying. >> >> I'm wondering what would be the best way to edit the >> data. I've often tried >> to edit the wm.vol, but this doesn't seem to fix >> anything. For the most >> part, the wm.vol is correct to begin with, but the >> wm cutting line isn't >> segmenting with the wm.vol. I've also tried to add >> control points but this >> doesn't seem to improve anything either. >> >> I've attached an image which I hope will further >> explain my problems. >> >> Thanks for any help >> >> >> > _______________________________________________ > 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. > >
_______________________________________________ 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.
