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
