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Dear All,
I would like to extract cortical envelop from my subjects T1 images to use later on for a source reconstruction in on their EEG data. I would like to use Power et al (2011)'s atlas with 264 regions. I am pretty new to Freesurfer and my search through the mailing list and tutorials confused me very much. So I would really appreciate if anyone could explain using a custom atlas to me or direct me to the sources that I can follow please.
So I have 2 questions regarding that. 1. Is there any chance that you could direct me step by step how to do this with Freesurfer.
2. While I am running extraction with Freesurfer, should I be using ROI nifti files in MNI coordinate or should I be using ROI nifti files that were inverse normalised to subject's native space?
I would really appreciate if you could help me with this please.
Thank you very much in advance
Kind regards Mina
External Email - Use Caution
Dear All,
I know it is a very basic question but I would really appreciate if I can get any support for source or recommendations about how could I extract custom atlas based surface segmentation using Power et al(2011) atlas please.
Thank you very much in advance,
Mina
On Thu, Apr 4, 2019 at 3:22 PM Mina Shire minashirely@gmail.com wrote:
Dear All,
I would like to extract cortical envelop from my subjects T1 images to use later on for a source reconstruction in on their EEG data. I would like to use Power et al (2011)'s atlas with 264 regions. I am pretty new to Freesurfer and my search through the mailing list and tutorials confused me very much. So I would really appreciate if anyone could explain using a custom atlas to me or direct me to the sources that I can follow please.
So I have 2 questions regarding that.
- Is there any chance that you could direct me step by step how to do
this with Freesurfer.
- While I am running extraction with Freesurfer, should I be using ROI
nifti files in MNI coordinate or should I be using ROI nifti files that were inverse normalised to subject's native space?
I would really appreciate if you could help me with this please.
Thank you very much in advance
Kind regards Mina
Hi Mina
I'm not sure about the Power atlas question, but for us the best thing to do is stay as close to the scanner data as possible. Ideally dicoms that came off the scanner, but alternatively nifti images made from them. Transforming to MNI coords will reduce your effective resolution, and inverse transforming will reduce it again, so I definitely wouldn't do that.
cheers Bruce On Mon, 8 Apr 2019, Mina Shire wrote:
External Email - Use Caution
Dear All, I know it is a very basic question but I would really appreciate if I can get any support for source or recommendations about how could I extract custom atlas based surface segmentation using Power et al(2011) atlas please.
Thank you very much in advance,
Mina
On Thu, Apr 4, 2019 at 3:22 PM Mina Shire minashirely@gmail.com wrote: Dear All, I would like to extract cortical envelop from my subjects T1 images to use later on for a source reconstruction in on their EEG data. I would like to use Power et al (2011)'s atlas with 264 regions. I am pretty new to Freesurfer and my search through the mailing list and tutorials confused me very much. So I would really appreciate if anyone could explain using a custom atlas to me or direct me to the sources that I can follow please.
So I have 2 questions regarding that.
Is there any chance that you could direct me step by step how to do this with Freesurfer.
While I am running extraction with Freesurfer, should I be using ROI nifti files in MNI
coordinate or should I be using ROI nifti files that were inverse normalised to subject's native space?
I would really appreciate if you could help me with this please.
Thank you very much in advance
Kind regards Mina
External Email - Use Caution
An updated version of the Power parcellation is available on the FS_LR atlas mesh in the BALSA database:
https://balsa.wustl.edu/file/show/JX5V
You can run FreeSurfer on your subject¹s T1w images and then either bring the data onto FS_LR or the atlas onto fsaverage using the instructions available here:
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&a... t=8&ved=2ahUKEwiOhOXxtsHhAhWBTd8KHXH7CgkQFjAAegQIABAC&url=https%3A%2F%2Fwik i.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-Free Surfer-HCP.pdf&usg=AOvVaw2wx1IdlCJFJxczsj8QEw4l
No need to worry about the limitations of MNI space that Bruce mentions.
Matt.
On 4/8/19, 3:40 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Mina
I'm not sure about the Power atlas question, but for us the best thing to do is stay as close to the scanner data as possible. Ideally dicoms that came off the scanner, but alternatively nifti images made from them. Transforming to MNI coords will reduce your effective resolution, and inverse transforming will reduce it again, so I definitely wouldn't do that.
cheers Bruce On Mon, 8 Apr 2019, Mina Shire wrote:
External Email - Use CautionDear All, I know it is a very basic question but I would really appreciate if I can get any support for source or recommendations about how could I extract custom atlas based surface segmentation using Power et al(2011) atlas please.
Thank you very much in advance,
Mina
On Thu, Apr 4, 2019 at 3:22 PM Mina Shire minashirely@gmail.com wrote: Dear All, I would like to extract cortical envelop from my subjects T1 images to use later on for a source reconstruction in on their EEG data. I would like to use Power et al (2011)'s atlas with 264 regions. I am pretty new to Freesurfer and my search through the mailing list and tutorials confused me very much. So I would really appreciate if anyone could explain using a custom atlas to me or direct me to the sources that I can follow please.
So I have 2 questions regarding that.
- Is there any chance that you could direct me step by step how to do
this with Freesurfer.
- While I am running extraction with Freesurfer, should I be using ROI
nifti files in MNI coordinate or should I be using ROI nifti files that were inverse normalised to subject's native space?
I would really appreciate if you could help me with this please.
Thank you very much in advance
Kind regards Mina
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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Thank you very much for both of your answers. I haven't been able to download the Power parcellation from BALSA webpage, even though I registered to the site, it doesn't allow to download, so I sent an email to the technical team. Once I download it I will follow the instructions Matt sent. Thank you very much indeed.
Mina
On Mon, Apr 8, 2019 at 10:24 PM Glasser, Matthew glasserm@wustl.edu wrote:
External Email - Use CautionAn updated version of the Power parcellation is available on the FS_LR atlas mesh in the BALSA database:
https://balsa.wustl.edu/file/show/JX5V
You can run FreeSurfer on your subject¹s T1w images and then either bring the data onto FS_LR or the atlas onto fsaverage using the instructions available here:
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&a... t=8&ved=2ahUKEwiOhOXxtsHhAhWBTd8KHXH7CgkQFjAAegQIABAC&url=https%3A%2F%2Fwik https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=2ahUKEwiOhOXxtsHhAhWBTd8KHXH7CgkQFjAAegQIABAC&url=https%3A%2F%2Fwik i.humanconnectome.org %2Fdownload%2Fattachments%2F63078513%2FResampling-Free Surfer-HCP.pdf&usg=AOvVaw2wx1IdlCJFJxczsj8QEw4l
No need to worry about the limitations of MNI space that Bruce mentions.
Matt.
On 4/8/19, 3:40 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Mina
I'm not sure about the Power atlas question, but for us the best thing to do is stay as close to the scanner data as possible. Ideally dicoms that came off the scanner, but alternatively nifti images made from them. Transforming to MNI coords will reduce your effective resolution, and inverse transforming will reduce it again, so I definitely wouldn't do that.
cheers Bruce On Mon, 8 Apr 2019, Mina Shire wrote:
External Email - Use CautionDear All, I know it is a very basic question but I would really appreciate if I can get any support for source or recommendations about how could I extract custom atlas based surface segmentation using Power et al(2011) atlas please.
Thank you very much in advance,
Mina
On Thu, Apr 4, 2019 at 3:22 PM Mina Shire minashirely@gmail.com
wrote:
Dear All,I would like to extract cortical envelop from my subjects T1 images to use later on for a source reconstruction in on their EEG data. I would like to use Power et al (2011)'s atlas with 264 regions. I am pretty new to Freesurfer and my search through the mailing list and tutorials confused me very much. So I would really appreciate if anyone could explain using a custom atlas to me or direct me to the sources that I can follow please.
So I have 2 questions regarding that.
- Is there any chance that you could direct me step by step how to do
this with Freesurfer.
- While I am running extraction with Freesurfer, should I be using ROI
nifti files in MNI coordinate or should I be using ROI nifti files that were inverse normalised to subject's native space?
I would really appreciate if you could help me with this please.
Thank you very much in advance
Kind regards Mina
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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Mina Shire