Hey Bruce, Thanks so much. If it would help, I could upload another subject, perhaps one with worse segmentation in the occipital lobe. I could also upload a raw T1 image sequence (Nifiti)
Matt On Wed, Aug 6, 2014 at 9:48 AM, Tirrell, Lee <ltirr...@mgh.harvard.edu> wrote: > Hi Matt, > > I've taken a look at the subject that you uploaded. I initially deleted > portions of the skull from the brainmask that weren't removed from coronal > slices 101-109 (see screenshot), which led to some improvement. I also > edited the wm volume by deleting areas that were obviously not white > matter, even if it didn't effect the white matter surface. However, this > didn't lead to much improvement. The segmentation isn't as bad in this > subject as in the screenshot that you sent originally, so this strategy may > help in worse cases. > > I am going to take another look at it now to try to improve the > segmentation further. > > Best, > Lee > > > On 07/30/2014 12:21 PM, Walton, Matt wrote: > > 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. >>> >>> >> > > > _______________________________________________ > 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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