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
