[Freesurfer] Research Assistant for Brain Imaging Studies @ Albert Einstein College of Medicine {Disarmed}

[Emily Schwartz]

External Email - Use Caution

The Position:

The Research Assistant will work in the Division of Cognitive and Motor Aging 
to acquire, manage and process behavioral and brain imaging data in ongoing 
neuroimaging studies of older adults.
Responsibilities
•   Recruit, screen and accompany older adults to brain imaging studies
•   Acquire and enter behavioral data into paper and computerized forms, 
review forms for completeness and accuracy
•   Maintain computer databases of behavioral and brain imaging data
•   Read, process, and quality check brain imaging data
Qualifications
•   Bachelor's Degree required
• Coursework in Neuroscience, Neuroanatomy, Cognitive Science/Psychology, 
or Computer science preferred

Skills and Competencies

•   Outstanding interpersonal and computing skills required
•   Strong database management, and clear understanding of clinical and 
research databases highly preferred
•   Previous experience with neuroimaging processing highly preferred.
•   Proficiency in neuroimaging processing software (FreeSurfer, fsl, SPM) 
preferred
•   Previous experience with Linux operating systems and MATLAB software 
preferred

APPLY HERE:

https://careers-einstein.icims.com/jobs/11910/psychology-assistant/job?mobile=false=950=500=true=false=-300=-240

Helena M. Blumen, PhD.
Assistant Professor
Department of Medicine (Geriatrics)
Department of Neurology (Cognitive and Motor Aging)
Albert Einstein College of Medicine
E-mail: helena.blu...@einstein.yu.edu
Office Phone: (718) 430 3810
http://www.einstein.yu.edu/faculty/12983/helena-blumen/

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Re: [Freesurfer] Hippocampal subfield version

[Emily Schwartz]

External Email - Use Caution

Hi Eugenio,

Thanks! I am able to run it now.

Best,
Emily

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, 
Eugenio [e.igles...@ucl.ac.uk]
Sent: Thursday, April 11, 2019 1:07 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfield version


External Email - Use Caution
Hi Emily,
I suspect that you’re mixing versions. Please make sure that you source the dev 
version.
Cheers,
/E

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Emily Schwartz 

Reply-To: Freesurfer support list 
Date: Thursday, 11 April 2019 at 13:02
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal subfield version


External Email - Use Caution
Hi Eugenio,

Thank you so much. I downloaded the development version, but when I run
"segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]," 
it says command not found.

After I download the runtime2014 version, I get the MCRv84 folder, but when I 
try to run a subject through the hippocampal subfield it gives me an error and 
tells me to download runtime2012b. Once I do that I also get the MCRv80 folder 
and am able to run the hippocampal segmentation, but I assume this is the 2017 
version since I cannot run the amygdala segmentation. I am not sure what I am 
doing wrong when I download the 2018 dev version.

Best,
Emily

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, 
Eugenio [e.igles...@ucl.ac.uk]
Sent: Thursday, April 04, 2019 5:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfield version

External Email - Use Caution
Hi Emily,
You need to download the dev version, but run the subfield/amygdala volume on 
cases reconned with FS6.0.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Emily Schwartz 

Reply-To: Freesurfer support list 
Date: Wednesday, 3 April 2019 at 15:44
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfield version


External Email - Use Caution
Hello FS experts,

I was planning to use the hippocampal subfield segmentation module in 
FreeSurfer 6.0 on a Linux ubuntu computer. I also would like to use the nuclei 
of the amygdala segmentation, but realized I need to download the development 
version in order to do that. Is there any reason why I shouldn't use the 
development version over the 6.0 release?

Thank you in advance.

Best,
Emily


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Re: [Freesurfer] Hippocampal subfield version

[Emily Schwartz]

External Email - Use Caution

Hi Eugenio,

Thank you so much. I downloaded the development version, but when I run
"segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]," 
it says command not found.

After I download the runtime2014 version, I get the MCRv84 folder, but when I 
try to run a subject through the hippocampal subfield it gives me an error and 
tells me to download runtime2012b. Once I do that I also get the MCRv80 folder 
and am able to run the hippocampal segmentation, but I assume this is the 2017 
version since I cannot run the amygdala segmentation. I am not sure what I am 
doing wrong when I download the 2018 dev version.

Best,
Emily

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, 
Eugenio [e.igles...@ucl.ac.uk]
Sent: Thursday, April 04, 2019 5:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfield version


External Email - Use Caution
Hi Emily,
You need to download the dev version, but run the subfield/amygdala volume on 
cases reconned with FS6.0.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Emily Schwartz 

Reply-To: Freesurfer support list 
Date: Wednesday, 3 April 2019 at 15:44
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfield version


External Email - Use Caution
Hello FS experts,

I was planning to use the hippocampal subfield segmentation module in 
FreeSurfer 6.0 on a Linux ubuntu computer. I also would like to use the nuclei 
of the amygdala segmentation, but realized I need to download the development 
version in order to do that. Is there any reason why I shouldn't use the 
development version over the 6.0 release?

Thank you in advance.

Best,
Emily


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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] Hippocampal subfield version

[Emily Schwartz]

External Email - Use Caution

Hello FS experts,

I was planning to use the hippocampal subfield segmentation module in 
FreeSurfer 6.0 on a Linux ubuntu computer. I also would like to use the nuclei 
of the amygdala segmentation, but realized I need to download the development 
version in order to do that. Is there any reason why I shouldn't use the 
development version over the 6.0 release?

Thank you in advance.

Best,
Emily


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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Surface Errors

[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

[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

[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

[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

[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.
>
>
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Re: [Freesurfer] Surface Errors

[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] Wm.mgz editing

[Emily Schwartz]

Hi Bruce,

Thanks for getting back to me. I am trying to upload the data via ftp, but I 
either get the error " 200 PORT command successful. Consider using PASV. 553 
Could not create file." or when I try epsv "?Invalid command."

Here is the session history:

Name (surfer.nmr.mgh.harvard.edu:admin): anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> put /home/admin/Desktop/FS_data_1.zip
local: /home/admin/Desktop/FS_data_1.zip remote: 
/home/admin/Desktop/FS_data_1.zip
200 PORT command successful. Consider using PASV.
553 Could not create file.
ftp> EPSV
?Invalid command
ftp> PASV
?Invalid command
ftp> ls 
200 PORT command successful. Consider using PASV.
150 Here comes the directory listing.
226 Transfer done (but failed to open directory).
ftp> pwd
257 "/transfer/incoming"
ftp> put /home/admin/Desktop/FS_data_1.zip
local: /home/admin/Desktop/FS_data_1.zip remote: 
/home/admin/Desktop/FS_data_1.zip
200 PORT command successful. Consider using PASV.
553 Could not create file.
ftp> PASV
?Invalid command
ftp> pasv
?Invalid command
ftp> cd /home/admin/Desktop
550 Failed to change directory.
ftp> 

Do you have any advice on how to fix this? 

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: Thursday, February 08, 2018 11:16 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Wm.mgz editing

Probably a topological defect but we would need the data to tell. Feel free to 
ftp it to us and we will take a look
Cheers
Bruce

> On Feb 8, 2018, at 12:19 PM, Emily Schwartz <emily.schwa...@einstein.yu.edu> 
> wrote:
>
> Hi FreeSurfer community,
>
> I am relatively new to manually editing and am having some questions dealing 
> with editing the wm.mgz. Occasionally, white matter and grey matter are being 
> incorrectly cut out, but I cannot edit WM voxels in the area (lh postcentral) 
> because they are already considered WM in the heat map (but excluded from the 
> boundary). I have attached images. How would I go about fixing this? Would 
> control points work here?
>
> And would the segmentation error in slices 79-81(lh postcentral) be edited by 
> adding wm voxels (I can't really add any to slice 79)?
>
> (This is an elderly brain.)
>
> Thank you,
>
> Emily
>
>
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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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.


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