Hey Bruce, I uploaded a subject that you requested a few days ago (problems with segmentation in the occipital lobe). I just wanted to make sure the file transferred successfully, and if you have had a change to analyze.
Thanks, Matt On Mon, Jul 28, 2014 at 5:48 PM, Walton, Matt <mt.wal...@alumni.uleth.ca> wrote: > 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. >> >> >
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