Is there command in freesurfer that applies the linear transform (I suppose talairach.xfm) to brainmask.mgz to get the registered image?

 

Best,

Yi

 

 

No, it is in native individual space. We compute a linear transform but do not apply it

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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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