External Email - Use Caution
Hi Douglas,
I ran mri_convert --apply_transform talairach.xfm brainmask.mgz brainmask.talairach.mgz
But brainmask.talairach.mgz is all black. No error was thrown during talairach transformation computation. Could you help to check what's going on here? I attached 4 relevant files in the mail.
Thanks and best regards, 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.