I'm a little surprised you are getting them so frequently. Can you upload a couple of subjects so I can take a look?
On 02/21/2018 02:52 PM, Emily Schwartz wrote: > Hi Doug, > > I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors so > often? > > Best, > > Emily > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, February 21, 2018 2:18 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Surface Errors > > btw, what verions of FS are you using? > > > On 02/21/2018 01:25 PM, Emily Schwartz wrote: >> Got it, thank you so much! >> >> Best, >> >> Emily >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Wednesday, February 21, 2018 10:23 AM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Surface Errors >> >> Hi Emily >> >> it is a segmentation error, but it's a pretty small one. It will mess up >> the thickness in a region a few mm^2. You could fix it by editing the >> wm.mgz if you really care about that spot >> >> cheers >> Bruce >> >> >> On Wed, 21 Feb 2018, Emily Schwartz wrote: >> >>> Hi Doug, >>> >>> Thank you for getting back to me. I've attached two images (Slice165 and >>> Slice166) with an arrow pointing to the location. I am new at this, so >>> maybe I am wrong and it is not a segmentation error. >>> >>> I've also attached an additional image (Slice185) of what I think is a type >>> of topological error that I often see multiple times in a subject. Is this >>> a topological defect? If so, if it is only over 3 slices does it need to be >>> corrected? >>> >>> Thanks again, >>> >>> Emily >>> ________________________________ >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >>> [gr...@nmr.mgh.harvard.edu] >>> Sent: Tuesday, February 20, 2018 4:59 PM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Surface Errors >>> >>> sorry, what kind of errors? I could not really tell from the images what >>> the problem was >>> >>> >>> On 02/20/2018 10:22 AM, Emily Schwartz wrote: >>>> Hi FreeSurfer community, >>>> >>>> I am working on elderly subjects and have had this kind of surface error >>>> quite often in different locations. Usually, it's over about 3-4 slices >>>> (in one view) and can be fixed, but I am finding multiple in almost every >>>> subject and therefore taking a lot of time to edit (and then once >>>> reprocessed new ones sometimes come up in different locations). I was >>>> wondering if these are normal to have, minor surface errors that do not >>>> necessarily need to be fixed. I have added images of an example below. >>>> Here are some of the values I get from aparc.stats for caudal middle >>>> frontal lh after manually editing: >>>> >>>> Surface area: >>>> Original - 2500 mm^2 >>>> Edited - 2532 mm^2 >>>> >>>> Grey volume: >>>> Original - 1710 mm^3 >>>> Edited - 1727 mm^3 >>>> >>>> Thickness avg >>>> Original - 4455 mm std: 2.371 >>>> Edited - 4445 mm std: 2.365 >>>> >>>> Although the thickness values only differ by 10 mm, we are a little >>>> concerned because the difference is not within the standard deviation. >>>> >>>> Please let me know if all of these errors should be edited or if it may be >>>> okay to keep the smaller segmentation/topological errors as they are. >>>> >>>> Thank you, >>>> >>>> Emily >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
