Hi Tessa, you can use mri_vol2vol passing it the 4D time series volume and the BBR registration matrix and --fstarg. You will have to motion correct the time series (using the template from BBR as the target).
doug

On 10/5/11 6:02 AM, Tessa Dekker wrote:

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.dekker@ucl.ac.uk
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