External Email - Use Caution
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
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
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 dgreve@mgh.harvard.edu 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.
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 txli1@ualr.edu 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 dgreve@mgh.harvard.edu 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.
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 CautionDouglas,
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 txli1@ualr.edu 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 dgreve@mgh.harvard.edu 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
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 dgreve@mgh.harvard.edu 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 CautionDouglas,
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 txli1@ualr.edu 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 dgreve@mgh.harvard.edu
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
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
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 <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> 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 <txli1@ualr.edu <mailto:txli1@ualr.edu>> 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 <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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
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 dgreve@mgh.harvard.edu 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 CautionDouglas,
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 txli1@ualr.edu 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 dgreve@mgh.harvard.edu 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
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 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 txli1@ualr.edu 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 dgreve@mgh.harvard.edu 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 CautionDouglas,
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 txli1@ualr.edu 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 dgreve@mgh.harvard.edu 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
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%C2%A0) is the right way to go? Thanks for your time.
Best, Ting
On Apr 19, 2018, at 2:22 PM, Ting Li <txli1@ualr.edu mailto:txli1@ualr.edu> 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 <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> 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 <txli1@ualr.edu mailto:txli1@ualr.edu> 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 <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> 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 > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 wiki and the papers :)
On 04/19/2018 03:22 PM, Ting Li wrote:
External Email - Use CautionDouglas,
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 dgreve@mgh.harvard.edu 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 CautionDouglas,
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 txli1@ualr.edu 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 dgreve@mgh.harvard.edu 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dgreve@mgh.harvard.edu wrote:
The wiki and the papers :)
On 04/19/2018 03:22 PM, Ting Li wrote:
External Email - Use CautionDouglas,
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 dgreve@mgh.harvard.edu 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 CautionDouglas,
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 txli1@ualr.edu 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 dgreve@mgh.harvard.edu 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
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
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 dgreve@mgh.harvard.edu 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@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Khoi Mai -
Ting Li