They use different atlases
On 9/15/2020 2:32 PM, Yi Li wrote:
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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
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