Re: [Freesurfer] Finding Duplicate Subjects in a Database

2017-09-11 Thread Douglas N Greve
No, you at least have to run it through autorecon2


On 09/11/2017 04:06 PM, Sherrill, John T wrote:
> Sounds good. Unfortunately when I open many of my files that do not contain 
> an aseg file.  Many only have a scripts directory and nothing else. Is there 
> a way to process the files to just get the aseg data without doing a 
> recon-all?
>
> John Sherrill
> jtsherr...@uams.edu
> john_sherr...@me.com
> (870) 761-0580
>
> 
> 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, September 11, 2017 2:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Finding Duplicate Subjects in a Database
>
> Yea, that's what I would do. You can run asegstats2table to get a list
> of the volume for all ROIs (so this gives you a matrix of 550 by about
> 50). For each row (subject),  compare the volumes to that of every other
> row. You'll need to come up with a comparison function; maybe mean
> percent difference (you might need to exclude very small structures like
> optic chiasm, vessels, etc -- or only include certain structures like
> hippo, put, pal, lat vent, cerebellum, etc). Then rank all the subjects
> from lowest to highest difference and look at the ones with the lowest
> difference. You can probably think of other ways
>
>
> On 09/11/2017 03:17 PM, Sherrill, John T wrote:
>> I have run recon-all on all of the files. So I should start with 
>> asegstats2table ( 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_asegstats2table=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=MtJnnh5bFgsrOhtUjpvIR4hZ8YcefgfBG4f5F2sJI84=7l-5w5DwKzRbjsxDY-U40umkQFkb_J0u-1f06ML1V94=
>>   ) ?
>>
>> John Sherrill
>> jtsherr...@uams.edu
>> john_sherr...@me.com
>> (870) 761-0580
>>
>> 
>> 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, September 11, 2017 2:07 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Finding Duplicate Subjects in a Database
>>
>> One way is to perform a 6DOF registration between each pair. It is a lot
>> of pairs, but I don't think you can avoid it. Pairs that come from the
>> same subject will have an abnormally high (or low) objective function.
>> You could use mri_coreg (use --no-smooth) . If you've already run all
>> 550 through FS, then you might be able to look a the aseg.stats for
>> similar subjects.
>>
>>
>> On 09/11/2017 02:50 PM, Sherrill, John T wrote:
>>> I am trying to find the best way to identify likely duplicate subjects
>>> with in a database of about 550 subjects. Some subjects where
>>> duel-consented for studies and had multiple scans over a relatively
>>> short period of time. What is the best way to tease these out?
>>>
>>> John Sherrill
>>> jtsherr...@uams.edu
>>> john_sherr...@me.com
>>> (870) 761-0580
>>> 
>>> Confidentiality Notice: This e-mail message, including any
>>> attachments, is for the sole use of the intended recipient(s) and may
>>> contain confidential and privileged information. Any unauthorized
>>> review, use, disclosure or distribution is prohibited. If you are not
>>> the intended recipient, please contact the sender by reply e-mail and
>>> destroy all copies of the original message.
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=3njeh9IV2-mOyQ5jJRFboeitp92qUpuOvYjURKAMuB8=
>> --
>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4

Re: [Freesurfer] Finding Duplicate Subjects in a Database

2017-09-11 Thread Sherrill, John T
Sounds good. Unfortunately when I open many of my files that do not contain an 
aseg file.  Many only have a scripts directory and nothing else. Is there a way 
to process the files to just get the aseg data without doing a recon-all?

John Sherrill
jtsherr...@uams.edu
john_sherr...@me.com
(870) 761-0580


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, September 11, 2017 2:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Finding Duplicate Subjects in a Database

Yea, that's what I would do. You can run asegstats2table to get a list
of the volume for all ROIs (so this gives you a matrix of 550 by about
50). For each row (subject),  compare the volumes to that of every other
row. You'll need to come up with a comparison function; maybe mean
percent difference (you might need to exclude very small structures like
optic chiasm, vessels, etc -- or only include certain structures like
hippo, put, pal, lat vent, cerebellum, etc). Then rank all the subjects
from lowest to highest difference and look at the ones with the lowest
difference. You can probably think of other ways


On 09/11/2017 03:17 PM, Sherrill, John T wrote:
> I have run recon-all on all of the files. So I should start with 
> asegstats2table ( 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_asegstats2table=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=MtJnnh5bFgsrOhtUjpvIR4hZ8YcefgfBG4f5F2sJI84=7l-5w5DwKzRbjsxDY-U40umkQFkb_J0u-1f06ML1V94=
>   ) ?
>
> John Sherrill
> jtsherr...@uams.edu
> john_sherr...@me.com
> (870) 761-0580
>
> 
> 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, September 11, 2017 2:07 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Finding Duplicate Subjects in a Database
>
> One way is to perform a 6DOF registration between each pair. It is a lot
> of pairs, but I don't think you can avoid it. Pairs that come from the
> same subject will have an abnormally high (or low) objective function.
> You could use mri_coreg (use --no-smooth) . If you've already run all
> 550 through FS, then you might be able to look a the aseg.stats for
> similar subjects.
>
>
> On 09/11/2017 02:50 PM, Sherrill, John T wrote:
>> I am trying to find the best way to identify likely duplicate subjects
>> with in a database of about 550 subjects. Some subjects where
>> duel-consented for studies and had multiple scans over a relatively
>> short period of time. What is the best way to tease these out?
>>
>> John Sherrill
>> jtsherr...@uams.edu
>> john_sherr...@me.com
>> (870) 761-0580
>> 
>> Confidentiality Notice: This e-mail message, including any
>> attachments, is for the sole use of the intended recipient(s) and may
>> contain confidential and privileged information. Any unauthorized
>> review, use, disclosure or distribution is prohibited. If you are not
>> the intended recipient, please contact the sender by reply e-mail and
>> destroy all copies of the original message.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=3njeh9IV2-mOyQ5jJRFboeitp92qUpuOvYjURKAMuB8=
> --
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=ZP1E4cAyh8LcgkvzL-jfBxt2V8sZYJd9UcZdkViEAAk=
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: 
> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=Mj9DAJaDWsk0JKAxs99YViYRgOnIG81THLDrpjx0zEM=
>
> ___
> Freesurfer mailing list
>

Re: [Freesurfer] Finding Duplicate Subjects in a Database

2017-09-11 Thread Douglas N Greve
Yea, that's what I would do. You can run asegstats2table to get a list 
of the volume for all ROIs (so this gives you a matrix of 550 by about 
50). For each row (subject),  compare the volumes to that of every other 
row. You'll need to come up with a comparison function; maybe mean 
percent difference (you might need to exclude very small structures like 
optic chiasm, vessels, etc -- or only include certain structures like 
hippo, put, pal, lat vent, cerebellum, etc). Then rank all the subjects 
from lowest to highest difference and look at the ones with the lowest 
difference. You can probably think of other ways


On 09/11/2017 03:17 PM, Sherrill, John T wrote:
> I have run recon-all on all of the files. So I should start with 
> asegstats2table ( https://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table ) 
> ?
>
> John Sherrill
> jtsherr...@uams.edu
> john_sherr...@me.com
> (870) 761-0580
>
> 
> 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, September 11, 2017 2:07 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Finding Duplicate Subjects in a Database
>
> One way is to perform a 6DOF registration between each pair. It is a lot
> of pairs, but I don't think you can avoid it. Pairs that come from the
> same subject will have an abnormally high (or low) objective function.
> You could use mri_coreg (use --no-smooth) . If you've already run all
> 550 through FS, then you might be able to look a the aseg.stats for
> similar subjects.
>
>
> On 09/11/2017 02:50 PM, Sherrill, John T wrote:
>> I am trying to find the best way to identify likely duplicate subjects
>> with in a database of about 550 subjects. Some subjects where
>> duel-consented for studies and had multiple scans over a relatively
>> short period of time. What is the best way to tease these out?
>>
>> John Sherrill
>> jtsherr...@uams.edu
>> john_sherr...@me.com
>> (870) 761-0580
>> 
>> Confidentiality Notice: This e-mail message, including any
>> attachments, is for the sole use of the intended recipient(s) and may
>> contain confidential and privileged information. Any unauthorized
>> review, use, disclosure or distribution is prohibited. If you are not
>> the intended recipient, please contact the sender by reply e-mail and
>> destroy all copies of the original message.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=3njeh9IV2-mOyQ5jJRFboeitp92qUpuOvYjURKAMuB8=
> --
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=ZP1E4cAyh8LcgkvzL-jfBxt2V8sZYJd9UcZdkViEAAk=
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: 
> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=Mj9DAJaDWsk0JKAxs99YViYRgOnIG81THLDrpjx0zEM=
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=3njeh9IV2-mOyQ5jJRFboeitp92qUpuOvYjURKAMuB8=
>
>
> 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
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>  

Re: [Freesurfer] Finding Duplicate Subjects in a Database

2017-09-11 Thread Sherrill, John T
I have run recon-all on all of the files. So I should start with 
asegstats2table ( https://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table ) ?

John Sherrill
jtsherr...@uams.edu
john_sherr...@me.com
(870) 761-0580


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, September 11, 2017 2:07 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Finding Duplicate Subjects in a Database

One way is to perform a 6DOF registration between each pair. It is a lot
of pairs, but I don't think you can avoid it. Pairs that come from the
same subject will have an abnormally high (or low) objective function.
You could use mri_coreg (use --no-smooth) . If you've already run all
550 through FS, then you might be able to look a the aseg.stats for
similar subjects.


On 09/11/2017 02:50 PM, Sherrill, John T wrote:
>
> I am trying to find the best way to identify likely duplicate subjects
> with in a database of about 550 subjects. Some subjects where
> duel-consented for studies and had multiple scans over a relatively
> short period of time. What is the best way to tease these out?
>
> John Sherrill
> jtsherr...@uams.edu
> john_sherr...@me.com
> (870) 761-0580
> 
> Confidentiality Notice: This e-mail message, including any
> attachments, is for the sole use of the intended recipient(s) and may
> contain confidential and privileged information. Any unauthorized
> review, use, disclosure or distribution is prohibited. If you are not
> the intended recipient, please contact the sender by reply e-mail and
> destroy all copies of the original message.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=3njeh9IV2-mOyQ5jJRFboeitp92qUpuOvYjURKAMuB8=

--
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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=ZP1E4cAyh8LcgkvzL-jfBxt2V8sZYJd9UcZdkViEAAk=
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: 
https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=Mj9DAJaDWsk0JKAxs99YViYRgOnIG81THLDrpjx0zEM=

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Re: [Freesurfer] Finding Duplicate Subjects in a Database

2017-09-11 Thread Douglas N Greve
One way is to perform a 6DOF registration between each pair. It is a lot 
of pairs, but I don't think you can avoid it. Pairs that come from the 
same subject will have an abnormally high (or low) objective function. 
You could use mri_coreg (use --no-smooth) . If you've already run all 
550 through FS, then you might be able to look a the aseg.stats for 
similar subjects.


On 09/11/2017 02:50 PM, Sherrill, John T wrote:
>
> I am trying to find the best way to identify likely duplicate subjects 
> with in a database of about 550 subjects. Some subjects where 
> duel-consented for studies and had multiple scans over a relatively 
> short period of time. What is the best way to tease these out?
>
> John Sherrill
> jtsherr...@uams.edu
> john_sherr...@me.com
> (870) 761-0580
> 
> Confidentiality Notice: This e-mail message, including any 
> attachments, is for the sole use of the intended recipient(s) and may 
> contain confidential and privileged information. Any unauthorized 
> review, use, disclosure or distribution is prohibited. If you are not 
> the intended recipient, please contact the sender by reply e-mail and 
> destroy all copies of the original message.
>
>
> ___
> 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

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[Freesurfer] Finding Duplicate Subjects in a Database

2017-09-11 Thread Sherrill, John T
I am trying to find the best way to identify likely duplicate subjects with in 
a database of about 550 subjects. Some subjects where duel-consented for 
studies and had multiple scans over a relatively short period of time. What is 
the best way to tease these out?

John Sherrill
jtsherr...@uams.edu
john_sherr...@me.com
(870) 761-0580

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