Re: [Freesurfer] Recon-all with custom atlas

[Ting Li]

External Email - Use Caution

Thanks for your patience with me. I am really appreciate. : )

Ting
> On Apr 19, 2018, at 3:14 PM, Douglas N. Greve  wrote:
> 
> The wiki and the papers :)
> 
> 
> On 04/19/2018 03:22 PM, Ting Li wrote:
>> External Email - Use Caution
>> 
>> Douglas,
>> 
>> Thanks for your quick response. If I only want the information of cortical 
>> thickness, surface area, volume for various cortical regions and LGI, then 
>> the Freesurfer template is good enough and I don’t need to apply my own 
>> template. This is really helpful. Is there any documents that you will 
>> recommend to get a better understanding about Freesurfer?
>> 
>> Thanks a lot.
>> 
>> Ting
>>> On Apr 19, 2018, at 12:39 PM, Douglas N. Greve  
>>> wrote:
>>> 
>>> If you want to do a surface-based analysis, then you don't need to have
>>> an accurate volume template. If you want to use a custom volume-based
>>> segmentation atlas, then you'll need to run gcatrain and gca-apply
>>> 
>>> 
>>> On 04/19/2018 01:28 PM, Ting Li wrote:
 External Email - Use Caution
 
 Douglas,
 
 Sorry for bother you again. Our group want to study a cohort children’s 
 brain using Freesurfer. We prefer to register our subjects to a custom 
 children template. The template basically is an average of all the 
 subjects we are going to study. It is constructed by ANTs. The format is 
 nii.gz. My questions is where I should mention this registration template 
 in the command Recon-all?  or how to get the cortical thickness, surface 
 area and volume for various cortical regions for all subjects and perform 
 the GLM analyses?
 
 In Freesurfer, there is a command of making own template for registration. 
 If I generate my template from there, how can I run recon-all for the next 
 to make sure my subjects all register to this template? and how to get the 
 cortical thickness, surface area and volume for various cortical regions 
 for all subjects and perform the GLM analyses?
 
 I really need your help for this. Thanks for your time.
 
 Best,
 Ting
> On Apr 19, 2018, at 11:42 AM, Ting Li  wrote:
> 
> Douglas,
> 
> Thank you so much for your response. My atlas is nii.gz format. What 
> should I do to get the cortical thickness, surface area and volume for 
> various cortical regions? Thanks in advance.
> 
> Best,
> Ting
> 
> 
>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve  
>> wrote:
>> 
>> Is the atlas in GCA format? If so, then you can use gca-apply
>> 
>> 
>> On 04/19/2018 10:09 AM, Ting Li wrote:
>>> Hi Freesurfer Experts,
>>> 
>>> We want to run recon-all with a custom atlas which is generated from
>>> ANTs multivariate template construction. What is the right procedure
>>> to run recon-all? Run recon-all to my atlas itself first and them use
>>> this output as a template or I use the custom template directly. I
>>> looked up your email database to search related topic and got lost. I
>>> have sent another email to your group and no response received. Please
>>> help me.
>>> 
>>> Thanks for you time. I look forward to hearing from you.
>>> 
>>> Best,
>>> Ting
>>> 
>>> 
>>> ___
>>> 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
>> 
>> 
>> 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
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>>> Freesurfer mailing list
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
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Re: [Freesurfer] Recon-all with custom atlas

[Douglas N. Greve]

The wiki and the papers :)


On 04/19/2018 03:22 PM, Ting Li wrote:
>  External Email - Use Caution
>
> Douglas,
>
> Thanks for your quick response. If I only want the information of cortical 
> thickness, surface area, volume for various cortical regions and LGI, then 
> the Freesurfer template is good enough and I don’t need to apply my own 
> template. This is really helpful. Is there any documents that you will 
> recommend to get a better understanding about Freesurfer?
>
> Thanks a lot.
>
> Ting
>> On Apr 19, 2018, at 12:39 PM, Douglas N. Greve  
>> wrote:
>>
>> If you want to do a surface-based analysis, then you don't need to have
>> an accurate volume template. If you want to use a custom volume-based
>> segmentation atlas, then you'll need to run gcatrain and gca-apply
>>
>>
>> On 04/19/2018 01:28 PM, Ting Li wrote:
>>>  External Email - Use Caution
>>>
>>> Douglas,
>>>
>>> Sorry for bother you again. Our group want to study a cohort children’s 
>>> brain using Freesurfer. We prefer to register our subjects to a custom 
>>> children template. The template basically is an average of all the subjects 
>>> we are going to study. It is constructed by ANTs. The format is nii.gz. My 
>>> questions is where I should mention this registration template in the 
>>> command Recon-all?  or how to get the cortical thickness, surface area and 
>>> volume for various cortical regions for all subjects and perform the GLM 
>>> analyses?
>>>
>>> In Freesurfer, there is a command of making own template for registration. 
>>> If I generate my template from there, how can I run recon-all for the next 
>>> to make sure my subjects all register to this template? and how to get the 
>>> cortical thickness, surface area and volume for various cortical regions 
>>> for all subjects and perform the GLM analyses?
>>>
>>> I really need your help for this. Thanks for your time.
>>>
>>> Best,
>>> Ting
 On Apr 19, 2018, at 11:42 AM, Ting Li  wrote:

 Douglas,

 Thank you so much for your response. My atlas is nii.gz format. What 
 should I do to get the cortical thickness, surface area and volume for 
 various cortical regions? Thanks in advance.

 Best,
 Ting


> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve  
> wrote:
>
> Is the atlas in GCA format? If so, then you can use gca-apply
>
>
> On 04/19/2018 10:09 AM, Ting Li wrote:
>> Hi Freesurfer Experts,
>>
>> We want to run recon-all with a custom atlas which is generated from
>> ANTs multivariate template construction. What is the right procedure
>> to run recon-all? Run recon-all to my atlas itself first and them use
>> this output as a template or I use the custom template directly. I
>> looked up your email database to search related topic and got lost. I
>> have sent another email to your group and no response received. Please
>> help me.
>>
>> Thanks for you time. I look forward to hearing from you.
>>
>> Best,
>> Ting
>>
>>
>> ___
>> 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
>
>
> 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
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Recon-all with custom atlas

[Douglas N. Greve]

That is, but since that wiki was written, I've written a script called 
make_folding_atlas. It takes quite a while to run through the 10 or so 
iterations. You might not need it as surface-based registration is much 
less sensitive to brain changes than volume-based.


On 04/19/2018 04:05 PM, Ting Li wrote:
>
>
> Douglas,
>
> I have one more question. Do I need an accurate surface template for 
> my surface-based analysis? Does this ( 
> https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates ) is 
> the right way to go? Thanks for your time.
>
> Best,
> Ting
>> On Apr 19, 2018, at 2:22 PM, Ting Li > > wrote:
>>
>> Douglas,
>>
>> Thanks for your quick response. If I only want the information of 
>> cortical thickness, surface area, volume for various cortical regions 
>> and LGI, then the Freesurfer template is good enough and I don’t need 
>> to apply my own template. This is really helpful. Is there any 
>> documents that you will recommend to get a better understanding about 
>> Freesurfer?
>>
>> Thanks a lot.
>>
>> Ting
>>> On Apr 19, 2018, at 12:39 PM, Douglas N. Greve 
>>> > wrote:
>>>
>>> If you want to do a surface-based analysis, then you don't need to have
>>> an accurate volume template. If you want to use a custom volume-based
>>> segmentation atlas, then you'll need to run gcatrain and gca-apply
>>>
>>>
>>> On 04/19/2018 01:28 PM, Ting Li wrote:
    External Email - Use Caution

 Douglas,

 Sorry for bother you again. Our group want to study a cohort 
 children’s brain using Freesurfer. We prefer to register our 
 subjects to a custom children template. The template basically is 
 an average of all the subjects we are going to study. It is 
 constructed by ANTs. The format is nii.gz. My questions is where I 
 should mention this registration template in the command Recon-all? 
  or how to get the cortical thickness, surface area and volume for 
 various cortical regions for all subjects and perform the GLM analyses?

 In Freesurfer, there is a command of making own template for 
 registration. If I generate my template from there, how can I run 
 recon-all for the next to make sure my subjects all register to 
 this template? and how to get the cortical thickness, surface area 
 and volume for various cortical regions for all subjects and 
 perform the GLM analyses?

 I really need your help for this. Thanks for your time.

 Best,
 Ting
> On Apr 19, 2018, at 11:42 AM, Ting Li  > wrote:
>
> Douglas,
>
> Thank you so much for your response. My atlas is nii.gz format. 
> What should I do to get the cortical thickness, surface area and 
> volume for various cortical regions? Thanks in advance.
>
> Best,
> Ting
>
>
>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve 
>> > wrote:
>>
>> Is the atlas in GCA format? If so, then you can use gca-apply
>>
>>
>> On 04/19/2018 10:09 AM, Ting Li wrote:
>>> Hi Freesurfer Experts,
>>>
>>> We want to run recon-all with a custom atlas which is generated from
>>> ANTs multivariate template construction. What is the right procedure
>>> to run recon-all? Run recon-all to my atlas itself first and 
>>> them use
>>> this output as a template or I use the custom template directly. I
>>> looked up your email database to search related topic and got 
>>> lost. I
>>> have sent another email to your group and no response received. 
>>> Please
>>> help me.
>>>
>>> Thanks for you time. I look forward to hearing from you.
>>>
>>> Best,
>>> Ting
>>>
>>>
>>> ___
>>> 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
>>
>>
>> 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

Re: [Freesurfer] Recon-all with custom atlas

[Ting Li]

External Email - Use Caution

Douglas,

I have one more question. Do I need an accurate surface template for my 
surface-based analysis? Does this ( 
https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates 
 ) is the 
right way to go? Thanks for your time.

Best,
Ting
> On Apr 19, 2018, at 2:22 PM, Ting Li  wrote:
> 
> Douglas,
> 
> Thanks for your quick response. If I only want the information of cortical 
> thickness, surface area, volume for various cortical regions and LGI, then 
> the Freesurfer template is good enough and I don’t need to apply my own 
> template. This is really helpful. Is there any documents that you will 
> recommend to get a better understanding about Freesurfer? 
> 
> Thanks a lot.
> 
> Ting 
>> On Apr 19, 2018, at 12:39 PM, Douglas N. Greve  
>> wrote:
>> 
>> If you want to do a surface-based analysis, then you don't need to have 
>> an accurate volume template. If you want to use a custom volume-based 
>> segmentation atlas, then you'll need to run gcatrain and gca-apply
>> 
>> 
>> On 04/19/2018 01:28 PM, Ting Li wrote:
>>>External Email - Use Caution
>>> 
>>> Douglas,
>>> 
>>> Sorry for bother you again. Our group want to study a cohort children’s 
>>> brain using Freesurfer. We prefer to register our subjects to a custom 
>>> children template. The template basically is an average of all the subjects 
>>> we are going to study. It is constructed by ANTs. The format is nii.gz. My 
>>> questions is where I should mention this registration template in the 
>>> command Recon-all?  or how to get the cortical thickness, surface area and 
>>> volume for various cortical regions for all subjects and perform the GLM 
>>> analyses?
>>> 
>>> In Freesurfer, there is a command of making own template for registration. 
>>> If I generate my template from there, how can I run recon-all for the next 
>>> to make sure my subjects all register to this template? and how to get the 
>>> cortical thickness, surface area and volume for various cortical regions 
>>> for all subjects and perform the GLM analyses?
>>> 
>>> I really need your help for this. Thanks for your time.
>>> 
>>> Best,
>>> Ting
 On Apr 19, 2018, at 11:42 AM, Ting Li  wrote:
 
 Douglas,
 
 Thank you so much for your response. My atlas is nii.gz format. What 
 should I do to get the cortical thickness, surface area and volume for 
 various cortical regions? Thanks in advance.
 
 Best,
 Ting
 
 
> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve  
> wrote:
> 
> Is the atlas in GCA format? If so, then you can use gca-apply
> 
> 
> On 04/19/2018 10:09 AM, Ting Li wrote:
>> Hi Freesurfer Experts,
>> 
>> We want to run recon-all with a custom atlas which is generated from
>> ANTs multivariate template construction. What is the right procedure
>> to run recon-all? Run recon-all to my atlas itself first and them use
>> this output as a template or I use the custom template directly. I
>> looked up your email database to search related topic and got lost. I
>> have sent another email to your group and no response received. Please
>> help me.
>> 
>> Thanks for you time. I look forward to hearing from you.
>> 
>> Best,
>> Ting
>> 
>> 
>> ___
>> 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
> 
> 
> 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
>> 
>> ___
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>> 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 

Re: [Freesurfer] Recon-all with custom atlas

[Ting Li]

External Email - Use Caution

Douglas,

Thanks for your quick response. If I only want the information of cortical 
thickness, surface area, volume for various cortical regions and LGI, then the 
Freesurfer template is good enough and I don’t need to apply my own template. 
This is really helpful. Is there any documents that you will recommend to get a 
better understanding about Freesurfer? 

Thanks a lot.

Ting 
> On Apr 19, 2018, at 12:39 PM, Douglas N. Greve  wrote:
> 
> If you want to do a surface-based analysis, then you don't need to have 
> an accurate volume template. If you want to use a custom volume-based 
> segmentation atlas, then you'll need to run gcatrain and gca-apply
> 
> 
> On 04/19/2018 01:28 PM, Ting Li wrote:
>> External Email - Use Caution
>> 
>> Douglas,
>> 
>> Sorry for bother you again. Our group want to study a cohort children’s 
>> brain using Freesurfer. We prefer to register our subjects to a custom 
>> children template. The template basically is an average of all the subjects 
>> we are going to study. It is constructed by ANTs. The format is nii.gz. My 
>> questions is where I should mention this registration template in the 
>> command Recon-all?  or how to get the cortical thickness, surface area and 
>> volume for various cortical regions for all subjects and perform the GLM 
>> analyses?
>> 
>> In Freesurfer, there is a command of making own template for registration. 
>> If I generate my template from there, how can I run recon-all for the next 
>> to make sure my subjects all register to this template? and how to get the 
>> cortical thickness, surface area and volume for various cortical regions for 
>> all subjects and perform the GLM analyses?
>> 
>> I really need your help for this. Thanks for your time.
>> 
>> Best,
>> Ting
>>> On Apr 19, 2018, at 11:42 AM, Ting Li  wrote:
>>> 
>>> Douglas,
>>> 
>>> Thank you so much for your response. My atlas is nii.gz format. What should 
>>> I do to get the cortical thickness, surface area and volume for various 
>>> cortical regions? Thanks in advance.
>>> 
>>> Best,
>>> Ting
>>> 
>>> 
 On Apr 19, 2018, at 11:28 AM, Douglas N. Greve  
 wrote:
 
 Is the atlas in GCA format? If so, then you can use gca-apply
 
 
 On 04/19/2018 10:09 AM, Ting Li wrote:
> Hi Freesurfer Experts,
> 
> We want to run recon-all with a custom atlas which is generated from
> ANTs multivariate template construction. What is the right procedure
> to run recon-all? Run recon-all to my atlas itself first and them use
> this output as a template or I use the custom template directly. I
> looked up your email database to search related topic and got lost. I
> have sent another email to your group and no response received. Please
> help me.
> 
> Thanks for you time. I look forward to hearing from you.
> 
> Best,
> Ting
> 
> 
> ___
> 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
 
 
 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
> 
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Re: [Freesurfer] Recon-all with custom atlas

[Douglas N. Greve]

No, I think that is it.


On 04/19/2018 02:07 PM, Khoi Mai wrote:
>
> External Email - Use Caution
>
> From what I read in the gctrain --help, does it only require 
> talairach_man.xfm and the manual segmentation files? Does it require 
> anything else for each subject?
>
> On Thu, Apr 19, 2018 at 12:39 PM, Douglas N. Greve 
> > wrote:
>
> If you want to do a surface-based analysis, then you don't need to
> have
> an accurate volume template. If you want to use a custom volume-based
> segmentation atlas, then you'll need to run gcatrain and gca-apply
>
>
> On 04/19/2018 01:28 PM, Ting Li wrote:
> >          External Email - Use Caution
> >
> > Douglas,
> >
> > Sorry for bother you again. Our group want to study a cohort
> children’s brain using Freesurfer. We prefer to register our
> subjects to a custom children template. The template basically is
> an average of all the subjects we are going to study. It is
> constructed by ANTs. The format is nii.gz. My questions is where I
> should mention this registration template in the command
> Recon-all?  or how to get the cortical thickness, surface area and
> volume for various cortical regions for all subjects and perform
> the GLM analyses?
> >
> > In Freesurfer, there is a command of making own template for
> registration. If I generate my template from there, how can I run
> recon-all for the next to make sure my subjects all register to
> this template? and how to get the cortical thickness, surface area
> and volume for various cortical regions for all subjects and
> perform the GLM analyses?
> >
> > I really need your help for this. Thanks for your time.
> >
> > Best,
> > Ting
> >> On Apr 19, 2018, at 11:42 AM, Ting Li  > wrote:
> >>
> >> Douglas,
> >>
> >> Thank you so much for your response. My atlas is nii.gz format.
> What should I do to get the cortical thickness, surface area and
> volume for various cortical regions? Thanks in advance.
> >>
> >> Best,
> >> Ting
> >>
> >>
> >>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve
> > wrote:
> >>>
> >>> Is the atlas in GCA format? If so, then you can use gca-apply
> >>>
> >>>
> >>> On 04/19/2018 10:09 AM, Ting Li wrote:
>  Hi Freesurfer Experts,
> 
>  We want to run recon-all with a custom atlas which is
> generated from
>  ANTs multivariate template construction. What is the right
> procedure
>  to run recon-all? Run recon-all to my atlas itself first and
> them use
>  this output as a template or I use the custom template
> directly. I
>  looked up your email database to search related topic and got
> lost. I
>  have sent another email to your group and no response
> received. Please
>  help me.
> 
>  Thanks for you time. I look forward to hearing from you.
> 
>  Best,
>  Ting
> 
> 
>  ___
>  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
> 
> >>>
> >>>
> >>> 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
> 
>
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> 

Re: [Freesurfer] Recon-all with custom atlas

[Khoi Mai]

External Email - Use Caution

From what I read in the gctrain --help, does it only require
talairach_man.xfm and the manual segmentation files? Does it require
anything else for each subject?

On Thu, Apr 19, 2018 at 12:39 PM, Douglas N. Greve 
wrote:

> If you want to do a surface-based analysis, then you don't need to have
> an accurate volume template. If you want to use a custom volume-based
> segmentation atlas, then you'll need to run gcatrain and gca-apply
>
>
> On 04/19/2018 01:28 PM, Ting Li wrote:
> >  External Email - Use Caution
> >
> > Douglas,
> >
> > Sorry for bother you again. Our group want to study a cohort children’s
> brain using Freesurfer. We prefer to register our subjects to a custom
> children template. The template basically is an average of all the subjects
> we are going to study. It is constructed by ANTs. The format is nii.gz. My
> questions is where I should mention this registration template in the
> command Recon-all?  or how to get the cortical thickness, surface area and
> volume for various cortical regions for all subjects and perform the GLM
> analyses?
> >
> > In Freesurfer, there is a command of making own template for
> registration. If I generate my template from there, how can I run recon-all
> for the next to make sure my subjects all register to this template? and
> how to get the cortical thickness, surface area and volume for various
> cortical regions for all subjects and perform the GLM analyses?
> >
> > I really need your help for this. Thanks for your time.
> >
> > Best,
> > Ting
> >> On Apr 19, 2018, at 11:42 AM, Ting Li  wrote:
> >>
> >> Douglas,
> >>
> >> Thank you so much for your response. My atlas is nii.gz format. What
> should I do to get the cortical thickness, surface area and volume for
> various cortical regions? Thanks in advance.
> >>
> >> Best,
> >> Ting
> >>
> >>
> >>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve 
> wrote:
> >>>
> >>> Is the atlas in GCA format? If so, then you can use gca-apply
> >>>
> >>>
> >>> On 04/19/2018 10:09 AM, Ting Li wrote:
>  Hi Freesurfer Experts,
> 
>  We want to run recon-all with a custom atlas which is generated from
>  ANTs multivariate template construction. What is the right procedure
>  to run recon-all? Run recon-all to my atlas itself first and them use
>  this output as a template or I use the custom template directly. I
>  looked up your email database to search related topic and got lost. I
>  have sent another email to your group and no response received. Please
>  help me.
> 
>  Thanks for you time. I look forward to hearing from you.
> 
>  Best,
>  Ting
> 
> 
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> >>> ___
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> >>> 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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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Recon-all with custom atlas

[Douglas N. Greve]

If you want to do a surface-based analysis, then you don't need to have 
an accurate volume template. If you want to use a custom volume-based 
segmentation atlas, then you'll need to run gcatrain and gca-apply


On 04/19/2018 01:28 PM, Ting Li wrote:
>  External Email - Use Caution
>
> Douglas,
>
> Sorry for bother you again. Our group want to study a cohort children’s brain 
> using Freesurfer. We prefer to register our subjects to a custom children 
> template. The template basically is an average of all the subjects we are 
> going to study. It is constructed by ANTs. The format is nii.gz. My questions 
> is where I should mention this registration template in the command 
> Recon-all?  or how to get the cortical thickness, surface area and volume for 
> various cortical regions for all subjects and perform the GLM analyses?
>
> In Freesurfer, there is a command of making own template for registration. If 
> I generate my template from there, how can I run recon-all for the next to 
> make sure my subjects all register to this template? and how to get the 
> cortical thickness, surface area and volume for various cortical regions for 
> all subjects and perform the GLM analyses?
>
> I really need your help for this. Thanks for your time.
>
> Best,
> Ting
>> On Apr 19, 2018, at 11:42 AM, Ting Li  wrote:
>>
>> Douglas,
>>
>> Thank you so much for your response. My atlas is nii.gz format. What should 
>> I do to get the cortical thickness, surface area and volume for various 
>> cortical regions? Thanks in advance.
>>
>> Best,
>> Ting
>>
>>
>>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve  
>>> wrote:
>>>
>>> Is the atlas in GCA format? If so, then you can use gca-apply
>>>
>>>
>>> On 04/19/2018 10:09 AM, Ting Li wrote:
 Hi Freesurfer Experts,

 We want to run recon-all with a custom atlas which is generated from
 ANTs multivariate template construction. What is the right procedure
 to run recon-all? Run recon-all to my atlas itself first and them use
 this output as a template or I use the custom template directly. I
 looked up your email database to search related topic and got lost. I
 have sent another email to your group and no response received. Please
 help me.

 Thanks for you time. I look forward to hearing from you.

 Best,
 Ting


 ___
 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
>>>
>>>
>>> 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

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Re: [Freesurfer] Recon-all with custom atlas

[Douglas N. Greve]

I'm not clear on what you are trying to do. Did you apply the atlas to 
an individual and have the atlas ROIs in the individual brain?


On 04/19/2018 12:42 PM, Ting Li wrote:
> 
> Douglas,
>
> Thank you so much for your response. My atlas is nii.gz format. What should I 
> do to get the cortical thickness, surface area and volume for various 
> cortical regions? Thanks in advance.
>
> Best,
> Ting
>
>
>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve  
>> wrote:
>>
>> Is the atlas in GCA format? If so, then you can use gca-apply
>>
>>
>> On 04/19/2018 10:09 AM, Ting Li wrote:
>>> Hi Freesurfer Experts,
>>>
>>> We want to run recon-all with a custom atlas which is generated from
>>> ANTs multivariate template construction. What is the right procedure
>>> to run recon-all? Run recon-all to my atlas itself first and them use
>>> this output as a template or I use the custom template directly. I
>>> looked up your email database to search related topic and got lost. I
>>> have sent another email to your group and no response received. Please
>>> help me.
>>>
>>> Thanks for you time. I look forward to hearing from you.
>>>
>>> Best,
>>> Ting
>>>
>>>
>>> ___
>>> 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
>>
>>
>> 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

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Re: [Freesurfer] Recon-all with custom atlas

[Ting Li]

External Email - Use Caution

Douglas,

Sorry for bother you again. Our group want to study a cohort children’s brain 
using Freesurfer. We prefer to register our subjects to a custom children 
template. The template basically is an average of all the subjects we are going 
to study. It is constructed by ANTs. The format is nii.gz. My questions is 
where I should mention this registration template in the command Recon-all?  or 
how to get the cortical thickness, surface area and volume for various cortical 
regions for all subjects and perform the GLM analyses? 

In Freesurfer, there is a command of making own template for registration. If I 
generate my template from there, how can I run recon-all for the next to make 
sure my subjects all register to this template? and how to get the cortical 
thickness, surface area and volume for various cortical regions for all 
subjects and perform the GLM analyses? 

I really need your help for this. Thanks for your time.

Best,
Ting
> On Apr 19, 2018, at 11:42 AM, Ting Li  wrote:
> 
> Douglas,
> 
> Thank you so much for your response. My atlas is nii.gz format. What should I 
> do to get the cortical thickness, surface area and volume for various 
> cortical regions? Thanks in advance. 
> 
> Best,
> Ting
> 
> 
>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve  
>> wrote:
>> 
>> Is the atlas in GCA format? If so, then you can use gca-apply
>> 
>> 
>> On 04/19/2018 10:09 AM, Ting Li wrote:
>>> Hi Freesurfer Experts,
>>> 
>>> We want to run recon-all with a custom atlas which is generated from 
>>> ANTs multivariate template construction. What is the right procedure 
>>> to run recon-all? Run recon-all to my atlas itself first and them use 
>>> this output as a template or I use the custom template directly. I 
>>> looked up your email database to search related topic and got lost. I 
>>> have sent another email to your group and no response received. Please 
>>> help me.
>>> 
>>> Thanks for you time. I look forward to hearing from you.
>>> 
>>> Best,
>>> Ting
>>> 
>>> 
>>> ___
>>> 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
>> 
>> 
>> 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] Recon-all with custom atlas

[Ting Li]

External Email - Use Caution

Douglas,

Thank you so much for your response. My atlas is nii.gz format. What should I 
do to get the cortical thickness, surface area and volume for various cortical 
regions? Thanks in advance. 

Best,
Ting


> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve  wrote:
> 
> Is the atlas in GCA format? If so, then you can use gca-apply
> 
> 
> On 04/19/2018 10:09 AM, Ting Li wrote:
>> Hi Freesurfer Experts,
>> 
>> We want to run recon-all with a custom atlas which is generated from 
>> ANTs multivariate template construction. What is the right procedure 
>> to run recon-all? Run recon-all to my atlas itself first and them use 
>> this output as a template or I use the custom template directly. I 
>> looked up your email database to search related topic and got lost. I 
>> have sent another email to your group and no response received. Please 
>> help me.
>> 
>> Thanks for you time. I look forward to hearing from you.
>> 
>> Best,
>> Ting
>> 
>> 
>> ___
>> 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
> 
> 
> 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] Recon-all with custom atlas

[Douglas N. Greve]

Is the atlas in GCA format? If so, then you can use gca-apply


On 04/19/2018 10:09 AM, Ting Li wrote:
> Hi Freesurfer Experts,
>
> We want to run recon-all with a custom atlas which is generated from 
> ANTs multivariate template construction. What is the right procedure 
> to run recon-all? Run recon-all to my atlas itself first and them use 
> this output as a template or I use the custom template directly. I 
> looked up your email database to search related topic and got lost. I 
> have sent another email to your group and no response received. Please 
> help me.
>
> Thanks for you time. I look forward to hearing from you.
>
> Best,
> Ting
>
>
> ___
> 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.