Dear experts,
I have analysed T1 data using Freesurfer. Now we have created atlas, template & tissue probability map using different methods and softwares. I need your help to use template in freesufer, so that we can compare with default template and our template. Please help me to put these images in appropriate folders in Freesurfer.
Thank you RB
Hi Ramesh
what are you trying to achieve? Our segmentation tools use their own format as they need information not contained in most standard images, so it won't be easy to get it into that format unless you use our training utility (mri_ca_train)
cheers Bruce On Thu, 11 Jan 2018, Ramesh Babu wrote:
Dear experts, I have analysed T1 data using Freesurfer. Now we have created atlas, template & tissue probability map using different methods and softwares. I need your help to use template in freesufer, so that we can compare with default template and our template. Please help me to put these images in appropriate folders in Freesurfer.
Thank you RB
Dear Bruce,
Thank you for your prompt response. I have 2 groups & 40 subjects in each groups in my study. I am using freesurfer and various other software for analysis. I found that the template available for registration either western or Chinese. There is no template available for Indian brain population. Therefore we want to develop a template specific to our population. And we have created templates using different software and want to compare the result with default template (western brain template) and our template. I need your help how to use this template in freesurfer. As you mentioned in the previous mail I will try with training utility (mri_ca_train). Can I get any user guide to know details about it?
Thank you Ramesh
On Thu, Jan 11, 2018 at 11:07 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Ramesh
what are you trying to achieve? Our segmentation tools use their own format as they need information not contained in most standard images, so it won't be easy to get it into that format unless you use our training utility (mri_ca_train)
cheers Bruce
On Thu, 11 Jan 2018, Ramesh Babu wrote:
Dear experts,
I have analysed T1 data using Freesurfer. Now we have created atlas, template & tissue probability map using different methods and softwares. I need your help to use template in freesufer, so that we can compare with default template and our template. Please help me to put these images in appropriate folders in Freesurfer.
Thank you RB
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.
Hi Ramesh
if you have segmentations in our aseg format (or edited asegs for that matter if you find them not accurate enough), you should be able to use mri_ca_train to genenerate a new .gca file and apply it to your subjects. Read the help and wiki and see if you can make it work, and let us knof i you have any issues. There are also surface-based atlases, but I suspect thos are a lot less likely to be biased by brain shape (since we map to a sphere anyway)
cheers Bruce On Fri, 12 Jan 2018, Ramesh Babu wrote:
Dear Bruce, Thank you for your prompt response. I have 2 groups & 40 subjects in each groups in my study. I am using freesurfer and various other software for analysis. I found that the template available for registration either western or Chinese. There is no template available for Indian brain population. Therefore we want to develop a template specific to our population. And we have created templates using different software and want to compare the result with default template (western brain template) and our template. I need your help how to use this template in freesurfer. As you mentioned in the previous mail I will try with training utility (mri_ca_train). Can I get any user guide to know details about it?
Thank you Ramesh
On Thu, Jan 11, 2018 at 11:07 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Ramesh
what are you trying to achieve? Our segmentation tools use their own format as they need information not contained in most standard images, so it won't be easy to get it into that format unless you use our training utility (mri_ca_train) cheers Bruce On Thu, 11 Jan 2018, Ramesh Babu wrote: Dear experts, I have analysed T1 data using Freesurfer. Now we have created atlas, template & tissue probability map using different methods and softwares. I need your help to use template in freesufer, so that we can compare with default template and our template. Please help me to put these images in appropriate folders in Freesurfer. Thank you RB
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.
you can use gcatrain (and jkgcatrain for testing) if you are using v6
On 1/12/18 3:27 PM, Bruce Fischl wrote:
Hi Ramesh
if you have segmentations in our aseg format (or edited asegs for that matter if you find them not accurate enough), you should be able to use mri_ca_train to genenerate a new .gca file and apply it to your subjects. Read the help and wiki and see if you can make it work, and let us knof i you have any issues. There are also surface-based atlases, but I suspect thos are a lot less likely to be biased by brain shape (since we map to a sphere anyway)
cheers Bruce On Fri, 12 Jan 2018, Ramesh Babu wrote:
Dear Bruce, Thank you for your prompt response. I have 2 groups & 40 subjects in each groups in my study. I am using freesurfer and various other software for analysis. I found that the template available for registration either western or Chinese. There is no template available for Indian brain population. Therefore we want to develop a template specific to our population. And we have created templates using different software and want to compare the result with default template (western brain template) and our template. I need your help how to use this template in freesurfer. As you mentioned in the previous mail I will try with training utility (mri_ca_train). Can I get any user guide to know details about it?
Thank you Ramesh
On Thu, Jan 11, 2018 at 11:07 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Ramesh
what are you trying to achieve? Our segmentation tools use their own format as they need information not contained in most standard images, so it won't be easy to get it into that format unless you use our training utility (mri_ca_train)
cheers Bruce On Thu, 11 Jan 2018, Ramesh Babu wrote:
Dear experts, I have analysed T1 data using Freesurfer. Now we have created atlas, template & tissue probability map using different methods and softwares. I need your help to use template in freesufer, so that we can compare with default template and our template. Please help me to put these images in appropriate folders in Freesurfer.
Thank you RB
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
Dear Bruce and Douglas,
Thank you for your suggestions. I am trying it and will need your suggestions on result.
Thank you Ramesh
On Fri, Jan 19, 2018 at 2:08 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
you can use gcatrain (and jkgcatrain for testing) if you are using v6
On 1/12/18 3:27 PM, Bruce Fischl wrote:
Hi Ramesh
if you have segmentations in our aseg format (or edited asegs for that matter if you find them not accurate enough), you should be able to use mri_ca_train to genenerate a new .gca file and apply it to your subjects. Read the help and wiki and see if you can make it work, and let us knof i you have any issues. There are also surface-based atlases, but I suspect thos are a lot less likely to be biased by brain shape (since we map to a sphere anyway)
cheers Bruce On Fri, 12 Jan 2018, Ramesh Babu wrote:
Dear Bruce, Thank you for your prompt response. I have 2 groups & 40 subjects in each groups in my study. I am using freesurfer and various other software for analysis. I found that the template available for registration either western or Chinese. There is no template available for Indian brain population. Therefore we want to develop a template specific to our population. And we have created templates using different software and want to compare the result with default template (western brain template) and our template. I need your help how to use this template in freesurfer. As you mentioned in the previous mail I will try with training utility (mri_ca_train). Can I get any user guide to know details about it?
Thank you Ramesh
On Thu, Jan 11, 2018 at 11:07 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu fischl@nmr.mgh.harvard.edu wrote: Hi Ramesh
what are you trying to achieve? Our segmentation tools use their ownformat as they need information not contained in most standard images, so it won't be easy to get it into that format unless you use our training utility (mri_ca_train)
cheers Bruce On Thu, 11 Jan 2018, Ramesh Babu wrote: Dear experts, I have analysed T1 data using Freesurfer. Now we have createdatlas, template & tissue probability map using different methods and softwares. I need your help to use template in freesufer, so that we can compare with default template and our template. Please help me to put these images in appropriate folders in Freesurfer.
Thank you RB
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 listFreesurfer@nmr.mgh.harvard.eduhttps://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.
Hey !
Is it possible not to receive the mails anymore ?
Best regards, Antoine
Le 11 janv. 2018 18:27, "Ramesh Babu" mgrameshbabu2013@gmail.com a écrit :
Dear experts,
I have analysed T1 data using Freesurfer. Now we have created atlas, template & tissue probability map using different methods and softwares. I need your help to use template in freesufer, so that we can compare with default template and our template. Please help me to put these images in appropriate folders in Freesurfer.
Thank you RB
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.
Take a look at the bottom of this page: https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On Feb 6, 2018, at 2:04 PM, Saturne Fox saturne.fox@gmail.com wrote:
Hey !
Is it possible not to receive the mails anymore ?
Best regards, Antoine
Le 11 janv. 2018 18:27, "Ramesh Babu" <mgrameshbabu2013@gmail.com mailto:mgrameshbabu2013@gmail.com> a écrit : Dear experts,
I have analysed T1 data using Freesurfer. Now we have created atlas, template & tissue probability map using different methods and softwares. I need your help to use template in freesufer, so that we can compare with default template and our template. Please help me to put these images in appropriate folders in Freesurfer.
Thank you RB
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 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@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Ramesh Babu -
Ricardo Valle -
Saturne Fox