Hi Emily, I looked over these subjects. While a few of the flagged spots are not really problems, most of them are true inaccuracies. I think the underlying problem is that your data is pretty noisy and have some ringing. What kind of acq was it? Scanner, field strength, pulse seq? Was it acquired at 1mm resolution or was it resampled? It looks a little blurry to me. What are the subject characteristics? I don't think there is an easy way to fix it. This might not be fatal as the errors are probably randomly distributed across space. If you have a good number of subjects, then there might not be much of an effect on group maps.
On 02/22/2018 02:50 PM, Emily Schwartz wrote: > Hi Doug, > > Attached are the point sets for the 3 subjects. For some issues, I put a > range of coordinate points. Let me know if you need anything else. > > Thanks! > > 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: Thursday, February 22, 2018 11:55 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Surface Errors > > got em. can you send me coordinates (col, row,slice) where you are > seeing the errors? You can also create a point set in FreeView (under > File->New PointSet) > > > On 02/22/2018 08:48 AM, Emily Schwartz wrote: >> Hi Doug, >> >> Great, thank you. I sent it to you via filedrop. >> >> 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 4:52 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Surface Errors >> >> yes, filedrop should be find >> >> thanks >> >> >> On 02/21/2018 04:44 PM, Emily Schwartz wrote: >>> Hi Doug, >>> >>> I definitely can. I cannot use FTP from this computer for some reason. Can >>> I upload it via filedrop and should I send it to your email? >>> >>> Thanks, >>> >>> 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 4:29 PM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Surface Errors >>> >>> 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 >>> >>> _______________________________________________ >>> 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 > > > _______________________________________________ > 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
