Hi Nameeta,

I'm wondering whether you could use FSL's flirt to do the normalization, but use the TTatlas as the -ref when you write out the output volume. Example:

This command registers generates an affine transform (.mat file) registering the avg152T1.hdr template to your individual (note that FSL recommends you use the clearest/best image as the ref image):

flirt -in avg152T1.hdr -ref my_individual.hdr -omat avg152_to_my_individual.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear

Now invert the matrix so it's your individual to avg152:

convert_xfm -matonly -omat my_individual_to_avg152.mat -inverse avg152_to_my_individual.mat

Now apply the matrix to my_individual.hdr, using TTatlas's bounding box, origin, etc:

flirt -in my_individual.hdr -applyxfm -init my_individual_to_avg152.mat -out my_individual+tlrc.hdr -paddingsize 0.0 -interp trilinear -ref TTatlas.hdr

I haven't tried this myself for the purposes you describe. Note also that you might need to play with the interp options to get a satisfactory result, depending on your input.

Donna