External Email - Use Caution
Hi,
I am a beginner of Freesurfer. I would be grateful if you could help me understand the excellent software.
I got brainmask.mgz at the end of autorecon1 and brain.mgz in the middle of autorecon2. Are these the images registered to MNI305 template?
In other words, is my understanding correct that brainmask.mgz is the image after orig.mgz is linearly registered to MNI305 (plus normalization and skullstripping), while brain.mgz is the image after normalized image is nonlinearly registered to MNI305 (plus cropping based on brainmask.mgz and further normalization)?
Thank you so much for your help in advance.
Best regards Yi Li
---
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
No, it is in native individual space. We compute a linear transform but do not apply it
On 9/15/2020 1:07 PM, Yi Li wrote:
External Email - Use Caution
Hi,
I am a beginner of Freesurfer. I would be grateful if you could help me understand the excellent software.
I got brainmask.mgz at the end of autorecon1 and brain.mgz in the middle of autorecon2. Are these the images registered to MNI305 template?
In other words, is my understanding correct that brainmask.mgz is the image after orig.mgz is linearly registered to MNI305 (plus normalization and skullstripping), while brain.mgz is the image after normalized image is nonlinearly registered to MNI305 (plus cropping based on brainmask.mgz and further normalization)?
Thank you so much for your help in advance.
Best regards
Yi Li
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Is there command in freesurfer that applies the linear transform (I suppose talairach.xfm) to brainmask.mgz to get the registered image?
Best, Yi
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve Sent: Tuesday, September 15, 2020 1:20 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL]Re: [Freesurfer] a question on Talairach transformation
No, it is in native individual space. We compute a linear transform but do not apply it On 9/15/2020 1:07 PM, Yi Li wrote:
External Email - Use Caution Hi,
I am a beginner of Freesurfer. I would be grateful if you could help me understand the excellent software.
I got brainmask.mgz at the end of autorecon1 and brain.mgz in the middle of autorecon2. Are these the images registered to MNI305 template?
In other words, is my understanding correct that brainmask.mgz is the image after orig.mgz is linearly registered to MNI305 (plus normalization and skullstripping), while brain.mgz is the image after normalized image is nonlinearly registered to MNI305 (plus cropping based on brainmask.mgz and further normalization)?
Thank you so much for your help in advance.
Best regards Yi Li
---
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
Try mri_convert --apply_transform talairach.xfm brainmask.mgz brainmask.mni305.mgz
On 9/15/2020 1:24 PM, Yi Li wrote:
External Email - Use Caution
Is there command in freesurfer that applies the linear transform (I suppose talairach.xfm) to brainmask.mgz to get the registered image?
Best,
Yi
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Douglas N. Greve *Sent:* Tuesday, September 15, 2020 1:20 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [EXTERNAL]Re: [Freesurfer] a question on Talairach transformation
No, it is in native individual space. We compute a linear transform but do not apply it
On 9/15/2020 1:07 PM, Yi Li wrote:
* External Email - Use Caution * Hi, I am a beginner of Freesurfer. I would be grateful if you could help me understand the excellent software. I got brainmask.mgz at the end of autorecon1 and brain.mgz in the middle of autorecon2. Are these the images registered to MNI305 template? In other words, is my understanding correct that brainmask.mgz is the image after orig.mgz is linearly registered to MNI305 (plus normalization and skullstripping), while brain.mgz is the image after normalized image is nonlinearly registered to MNI305 (plus cropping based on brainmask.mgz and further normalization)? Thank you so much for your help in advance. Best regards Yi Li --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. _______________________________________________ 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 email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks for the suggested command.
I am curious whether the following command also generates the transformation matrix in a different format (.lta format)? What is the difference between mri_em_register and talairach_avi which generates talairach.xfm?
mri_em_register brainmask.mgz $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta
-Yi From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve Sent: Tuesday, September 15, 2020 1:33 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL]Re: a question on Talairach transformation
Try mri_convert --apply_transform talairach.xfm brainmask.mgz brainmask.mni305.mgz
On 9/15/2020 1:24 PM, Yi Li wrote:
External Email - Use Caution Is there command in freesurfer that applies the linear transform (I suppose talairach.xfm) to brainmask.mgz to get the registered image?
Best, Yi
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve Sent: Tuesday, September 15, 2020 1:20 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL]Re: [Freesurfer] a question on Talairach transformation
No, it is in native individual space. We compute a linear transform but do not apply it On 9/15/2020 1:07 PM, Yi Li wrote:
External Email - Use Caution Hi,
I am a beginner of Freesurfer. I would be grateful if you could help me understand the excellent software.
I got brainmask.mgz at the end of autorecon1 and brain.mgz in the middle of autorecon2. Are these the images registered to MNI305 template?
In other words, is my understanding correct that brainmask.mgz is the image after orig.mgz is linearly registered to MNI305 (plus normalization and skullstripping), while brain.mgz is the image after normalized image is nonlinearly registered to MNI305 (plus cropping based on brainmask.mgz and further normalization)?
Thank you so much for your help in advance.
Best regards Yi Li
---
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
They use different atlases
On 9/15/2020 2:32 PM, Yi Li wrote:
External Email - Use Caution
Thanks for the suggested command.
I am curious whether the following command also generates the transformation matrix in a different format (.lta format)? What is the difference between mri_em_register and talairach_avi which generates talairach.xfm?
mri_em_register brainmask.mgz $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta
-Yi
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Douglas N. Greve *Sent:* Tuesday, September 15, 2020 1:33 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] [EXTERNAL]Re: a question on Talairach transformation
Try mri_convert --apply_transform talairach.xfm brainmask.mgz brainmask.mni305.mgz
On 9/15/2020 1:24 PM, Yi Li wrote:
* External Email - Use Caution * Is there command in freesurfer that applies the linear transform (I suppose talairach.xfm) to brainmask.mgz to get the registered image? Best, Yi *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Douglas N. Greve *Sent:* Tuesday, September 15, 2020 1:20 PM *To:* freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* [EXTERNAL]Re: [Freesurfer] a question on Talairach transformation No, it is in native individual space. We compute a linear transform but do not apply it On 9/15/2020 1:07 PM, Yi Li wrote: * External Email - Use Caution * Hi, I am a beginner of Freesurfer. I would be grateful if you could help me understand the excellent software. I got brainmask.mgz at the end of autorecon1 and brain.mgz in the middle of autorecon2. Are these the images registered to MNI305 template? In other words, is my understanding correct that brainmask.mgz is the image after orig.mgz is linearly registered to MNI305 (plus normalization and skullstripping), while brain.mgz is the image after normalized image is nonlinearly registered to MNI305 (plus cropping based on brainmask.mgz and further normalization)? Thank you so much for your help in advance. Best regards Yi Li --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. _______________________________________________ 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 email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. _______________________________________________ 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 email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
the em_reg command computes a linear transform to our internal atlas, which is loosely in MNI coords also, but not the official way we support reporting MNI ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yi Li Yi.Li@jax.org Sent: Tuesday, September 15, 2020 2:32 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL]Re: a question on Talairach transformation
External Email - Use Caution
Thanks for the suggested command.
I am curious whether the following command also generates the transformation matrix in a different format (.lta format)? What is the difference between mri_em_register and talairach_avi which generates talairach.xfm?
mri_em_register brainmask.mgz $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta
-Yi
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve Sent: Tuesday, September 15, 2020 1:33 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL]Re: a question on Talairach transformation
Try mri_convert --apply_transform talairach.xfm brainmask.mgz brainmask.mni305.mgz
On 9/15/2020 1:24 PM, Yi Li wrote:
External Email - Use Caution
Is there command in freesurfer that applies the linear transform (I suppose talairach.xfm) to brainmask.mgz to get the registered image?
Best,
Yi
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve Sent: Tuesday, September 15, 2020 1:20 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL]Re: [Freesurfer] a question on Talairach transformation
No, it is in native individual space. We compute a linear transform but do not apply it
On 9/15/2020 1:07 PM, Yi Li wrote:
External Email - Use Caution
Hi,
I am a beginner of Freesurfer. I would be grateful if you could help me understand the excellent software.
I got brainmask.mgz at the end of autorecon1 and brain.mgz in the middle of autorecon2. Are these the images registered to MNI305 template?
In other words, is my understanding correct that brainmask.mgz is the image after orig.mgz is linearly registered to MNI305 (plus normalization and skullstripping), while brain.mgz is the image after normalized image is nonlinearly registered to MNI305 (plus cropping based on brainmask.mgz and further normalization)?
Thank you so much for your help in advance.
Best regards
Yi Li
---
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
External Email - Use Caution
Thanks for the great explanations, Bruce and Greve.
-Yi
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Fischl, Bruce Sent: Tuesday, September 15, 2020 2:46 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL]Re: a question on Talairach transformation
the em_reg command computes a linear transform to our internal atlas, which is loosely in MNI coords also, but not the official way we support reporting MNI ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yi Li <Yi.Li@jax.orgmailto:Yi.Li@jax.org> Sent: Tuesday, September 15, 2020 2:32 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL]Re: a question on Talairach transformation
External Email - Use Caution
Thanks for the suggested command.
I am curious whether the following command also generates the transformation matrix in a different format (.lta format)? What is the difference between mri_em_register and talairach_avi which generates talairach.xfm?
mri_em_register brainmask.mgz $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta
-Yi
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve Sent: Tuesday, September 15, 2020 1:33 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL]Re: a question on Talairach transformation
Try mri_convert --apply_transform talairach.xfm brainmask.mgz brainmask.mni305.mgz
On 9/15/2020 1:24 PM, Yi Li wrote:
External Email - Use Caution
Is there command in freesurfer that applies the linear transform (I suppose talairach.xfm) to brainmask.mgz to get the registered image?
Best,
Yi
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve Sent: Tuesday, September 15, 2020 1:20 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL]Re: [Freesurfer] a question on Talairach transformation
No, it is in native individual space. We compute a linear transform but do not apply it
On 9/15/2020 1:07 PM, Yi Li wrote:
External Email - Use Caution
Hi,
I am a beginner of Freesurfer. I would be grateful if you could help me understand the excellent software.
I got brainmask.mgz at the end of autorecon1 and brain.mgz in the middle of autorecon2. Are these the images registered to MNI305 template?
In other words, is my understanding correct that brainmask.mgz is the image after orig.mgz is linearly registered to MNI305 (plus normalization and skullstripping), while brain.mgz is the image after normalized image is nonlinearly registered to MNI305 (plus cropping based on brainmask.mgz and further normalization)?
Thank you so much for your help in advance.
Best regards
Yi Li
---
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ---
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
Hi Yi LI
We compute the registration to MNI but don't apply it. So those images are in native coordinates.
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Yi Li Sent: Tuesday, September 15, 2020 1:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] a question on Talairach transformation
External Email - Use Caution Hi,
I am a beginner of Freesurfer. I would be grateful if you could help me understand the excellent software.
I got brainmask.mgz at the end of autorecon1 and brain.mgz in the middle of autorecon2. Are these the images registered to MNI305 template?
In other words, is my understanding correct that brainmask.mgz is the image after orig.mgz is linearly registered to MNI305 (plus normalization and skullstripping), while brain.mgz is the image after normalized image is nonlinearly registered to MNI305 (plus cropping based on brainmask.mgz and further normalization)?
Thank you so much for your help in advance.
Best regards Yi Li
---
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Fischl, Bruce -
Yi Li