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/

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