Re: [Freesurfer] Surface Errors

2018-02-26 Thread Emily Schwartz
Hi Doug,

They were initially reoriented for VBM analysis, but nothing else was changed 
(comparing original versus reoriented, there does not seem to be differences). 
The subjects are elderly (mean age = 74.08). We are investigating a new 
pre-dementia syndrome so there may be greater atrophy in some subjects, but the 
majority of the participants processed so far should be cognitively healthy.

MRI scanning was performed with a Philips 3T Achieva Quasar TX multinuclear 
MRI/MRS system equipped with a Dual Quasar High Performance Gradient System, 
32-channel broadband digital RF system, Quadrature T/R Head Coil, Rapid View 
reconstructor, Intera Achieva Scan-Tools Pro R2.5 Package, NetForum and 
ExamCards, and SENSE parallel imaging capability.

The T1-weighted whole head structural image was acquired using axial 3D-MP-RAGE 
parameters over a 240 mm FOV and 1.0 mm isotropic resolution, TE: 54.6 ms, TR: 
59.9 ms, with SENSE factor 2.5.
 
We really appreciate your help. Please let me know if you need any more info.

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: Monday, February 26, 2018 1:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Surface Errors

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.

Re: [Freesurfer] Surface Errors

2018-02-26 Thread Douglas N Greve
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

Re: [Freesurfer] Surface Errors

2018-02-22 Thread Emily Schwartz
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

Re: [Freesurfer] Surface Errors

2018-02-22 Thread Douglas N Greve
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 

Re: [Freesurfer] Surface Errors

2018-02-22 Thread Emily Schwartz
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

Re: [Freesurfer] Surface Errors

2018-02-21 Thread Douglas N Greve
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
>>>>>
>>>>> Thick

Re: [Freesurfer] Surface Errors

2018-02-21 Thread Emily Schwartz
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
>>&g

Re: [Freesurfer] Surface Errors

2018-02-21 Thread Douglas N Greve
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

Re: [Freesurfer] Surface Errors

2018-02-21 Thread Emily Schwartz
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


Re: [Freesurfer] Surface Errors

2018-02-21 Thread Emily Schwartz
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 

Re: [Freesurfer] Surface Errors

2018-02-21 Thread Douglas N Greve
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.
>>
>>
> __

Re: [Freesurfer] Surface Errors

2018-02-21 Thread Bruce Fischl
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


Re: [Freesurfer] Surface Errors

2018-02-20 Thread Douglas N Greve
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.