1. The way 4.5 works is to use the 1st image of the 1st run as the template for both motion correction and registration. All runs are then motion corrected to this template. The result is stored in bold/register.dat, so you can replace that with the result of bbregister. 2. See above. 3. Just use the 1st image of the 1st run
doug
ythomas wrote:
Hi,
I have finished the 4.5.0 fsfast tutorial, and am wondering about the structure-function registration part. Currently, the tutorial recommends: fslregister-sess -s mgh-101.1. I notice that a single register.dat is produced. How are the multiple runs being handled now? Is only the first run used or all the runs are automatically used?
I am asking because I would prefer to use bbregister. In bbregister, one passes to bbregister an anatomical subject id and a functional volume. So,
(1) Which functional volume should I give to bbregister? (2) Are the functional volumes of the different runs co-registered after I run "preproc-sess"? (3) Presumably, I should also give bbregister the pre-smoothed, but motion corrected functional volume since smoothing would remove the gray-white boundary distinction that bbregister uses?
Thanks, Thomas
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