Hi, I have used bbregister to register a set of partial volume fMRI time series to the subject structural (orig.mgz), which worked very well.
I now want to align each volume in each given time series to the orig.mgz. However, I've only managed to get one resampled volume, the target volume, out of bbregister at the time, making the full registration process rather lengthy. I have tried to align my fMRI time series to the orig.mgz by specifying the transformation matrices that I got from bbregister (both register.dat and the fsl compatible flirt.mtx) as input transformation matrix in various afni and FSL alignment scripts. Up until now however, none of my attempts have been successful because all these scripts seem to assume different transformation matrix conventions than bbregister...? Any advice on how to successfully align a whole fMRI time series to a 3D (non-standardised) subject scan, preferably using a bbregister transformation matrix, would be much appreciated. many thanks, Tessa -- Dept. Visual Neuroscience, UCL Institute of Ophthalmology 11-43 Bath Street London EC1V 9EL t.dek...@ucl.ac.uk
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