Yes, use mri_vol2vol, something like

mri_vol2vol --reg register.dat --mov flair.mgh --fstarg --o flair.anat.nii.gz

On 01/15/2014 05:10 PM, Arash Jalalian wrote:

Hi free surfer community,

I am trying to register Flair with T1 using bbregister and save the result as a volume so I can open it in my application that I am developing. I managed to obtain the register.dat and also to see the result using tkregister2. I was wondering if I can apply the transform provided in register.dat on a volume and save the output as mgz file.

Thanks, Arash

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