Hi Xiaojian, what is usually done is to run motion correction on your fMRI time series picking the middle time point as a reference. Then registration matrix for the middle time point will be appropriate for all the frames in the time series.

doug

XJ Kang wrote:

Dear Dr. Greve,

I am trying to apply "bbregister" to our EPI data after I read your 2009 Neuroimage paper "Accurate and robust brain image alignment using boundary-based registration".

One thing I found that bbregister will not save the coregistered information to the original --mov frame. Instread, it incorporated the info into "register.dat" or in the resampled "--o " image. Then I have to register all the EPI frames one by one and resampled them into the orig.mgz (256^3) space to compare them.

Is there any way or option that I can save the bbregistered frame (in low resolution EPI) in its own space? Then I can realign all other EPIs to this coregistered frame in the EPI resolution space.

Thank you for your time.

Sincerely, Xiaojian Kang