Hi all,
I want to visualize the directions of the fibers and therefore I try to construct a mean V1 image to overlay on the mean FA and mean skeleton.
1) I use vecreg with warp created for the FA images (-w FA_FA_to_target_warp) since vecreg does not allow for both linear and non-lineal inputs, is it ok to only use warp to target image? (or do I first need to register using the linear transformation and then the warp).
2) From the individual registered V1s I try to make a mean V1. I try this by first splitting the V1s in 3 volumes, add each volume across subjects in a 4D file (one for each of the three directions), separately average these 3 4D files across time (fslmaths –Tmean) and then merge the 3 average images in a 4D file. However, this mean V1 does not look very good, do I do something wrong?
Happy for any input,
Julian
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