Re: [Freesurfer] aparc+aseg.mgz for network analysis

[Jinsong Tang]

Thank you all so much!

That's great help!  I will use Matlab  to delete the other labels.

Best,

Jinsong


On Thu, Jul 21, 2016 at 11:48 AM, Douglas N Greve  wrote:

> That will binarize all the labels, but you could then use that as a mask
>
> On 07/21/2016 02:46 PM, Bruce Fischl wrote:
> > yes, that should work also
> > On Thu, 21 Jul 2016, Koubiyr, Ismail wrote:
> >
> >> I think you can use mri_binarize and set the match values as you like.
> >> Hope it can help.
> >>
> >> Best,
> >>
> >> Ismail
> >>
> >>> On Jul 21, 2016, at 2:13 PM, Jinsong Tang 
> wrote:
> >>>
> >>> Hello freesurfers,
> >>>
> >>> I want to select the subcortical structures (thalamus, pallidum,
> caudate, putamen, accumbens, hippocampus, and amygdala) and the 68 distinct
> brain regions as nodes of the individual brain networks. The labels are
> [9,11:13,17:18,26,48,50:54,58, 1002:1035, 2002:2035].  However, in the
> aparc+aseg.mgz files, there are also some other labels. Is there any way to
> delete all other unselected labels?
> >>>
> >>> Thank you so much!
> >>> Best,
> >>>
> >>> Jinsong
> >>> ___
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> >>> Freesurfer@nmr.mgh.harvard.edu
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> >>
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> >>
> >>
> >>
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> > Freesurfer@nmr.mgh.harvard.edu
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> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
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-- 
Jinsong Tang, MD
Institute of Mental Health
The Second Xiangya Hospital , Central South University
139 Renmin Road, Changsha Hunan 410011, P.R. China
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Re: [Freesurfer] aparc+aseg.mgz for network analysis

[Douglas N Greve]

That will binarize all the labels, but you could then use that as a mask

On 07/21/2016 02:46 PM, Bruce Fischl wrote:
> yes, that should work also
> On Thu, 21 Jul 2016, Koubiyr, Ismail wrote:
>
>> I think you can use mri_binarize and set the match values as you like.
>> Hope it can help.
>>
>> Best,
>>
>> Ismail
>>
>>> On Jul 21, 2016, at 2:13 PM, Jinsong Tang  wrote:
>>>
>>> Hello freesurfers,
>>>
>>> I want to select the subcortical structures (thalamus, pallidum, caudate, 
>>> putamen, accumbens, hippocampus, and amygdala) and the 68 distinct brain 
>>> regions as nodes of the individual brain networks. The labels are 
>>> [9,11:13,17:18,26,48,50:54,58, 1002:1035, 2002:2035].  However, in the 
>>> aparc+aseg.mgz files, there are also some other labels. Is there any way to 
>>> delete all other unselected labels?
>>>
>>> Thank you so much!
>>> Best,
>>>
>>> Jinsong
>>> ___
>>> 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
>>
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] aparc+aseg.mgz for network analysis

[Bruce Fischl]

yes, that should work also
On Thu, 21 Jul 2016, Koubiyr, Ismail wrote:

> I think you can use mri_binarize and set the match values as you like.
> Hope it can help.
>
> Best,
>
> Ismail
>
>> On Jul 21, 2016, at 2:13 PM, Jinsong Tang  wrote:
>>
>> Hello freesurfers,
>>
>> I want to select the subcortical structures (thalamus, pallidum, caudate, 
>> putamen, accumbens, hippocampus, and amygdala) and the 68 distinct brain 
>> regions as nodes of the individual brain networks. The labels are 
>> [9,11:13,17:18,26,48,50:54,58, 1002:1035, 2002:2035].  However, in the 
>> aparc+aseg.mgz files, there are also some other labels. Is there any way to 
>> delete all other unselected labels?
>>
>> Thank you so much!
>> Best,
>>
>> Jinsong
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] aparc+aseg.mgz for network analysis

[Koubiyr, Ismail]

I think you can use mri_binarize and set the match values as you like.
Hope it can help.

Best,

Ismail

> On Jul 21, 2016, at 2:13 PM, Jinsong Tang  wrote:
> 
> Hello freesurfers,
> 
> I want to select the subcortical structures (thalamus, pallidum, caudate, 
> putamen, accumbens, hippocampus, and amygdala) and the 68 distinct brain 
> regions as nodes of the individual brain networks. The labels are 
> [9,11:13,17:18,26,48,50:54,58, 1002:1035, 2002:2035].  However, in the 
> aparc+aseg.mgz files, there are also some other labels. Is there any way to 
> delete all other unselected labels?
> 
> Thank you so much!
> Best,
> 
> Jinsong
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] aparc+aseg.mgz for network analysis

[Bruce Fischl]

Hi Jinsong

you can either copy those labels out into their own volume using 
mri_extract_label, or use matlab to find the other labels and zero them out


cheers
Bruce


On Thu, 21 Jul 2016, Jinsong Tang wrote:


Hello freesurfers,

I want to select the subcortical structures (thalamus, pallidum, caudate, 
putamen,
accumbens, hippocampus, and amygdala) and the 68 distinct brain regions as 
nodes of
the individual brain networks. The labels are [9,11:13,17:18,26,48,50:54,58,
1002:1035, 2002:2035].  However, in the aparc+aseg.mgz files, there are also 
some
other labels. Is there any way to delete all other unselected labels?

Thank you so much!
Best,

Jinsong

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[Freesurfer] aparc+aseg.mgz for network analysis

[Jinsong Tang]

Hello freesurfers,

I want to select the subcortical structures (thalamus, pallidum, caudate,
putamen, accumbens, hippocampus, and amygdala) and the 68 distinct brain
regions as nodes of the individual brain networks. The labels are
[9,11:13,17:18,26,48,50:54,58, 1002:1035, 2002:2035].  However, in the
aparc+aseg.mgz files, there are also some other labels. Is there any way to
delete all other unselected labels?

Thank you so much!
Best,

Jinsong
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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
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