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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
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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.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:
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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:
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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
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