HI,
i am doing flirt regisstration of structural image to brain regions.i have done in 2 seps
1.maping template to subject image using flirt
>>>flirt -in /usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz -ref sE12001-0013-00001-000176-01.nii.gz -out atlastoimg -omat atlastoimg.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear

here sE12001-0013-00001-000176-01.nii.gz is subject image
and i got transformation matrix as :
0.02849413345 -0.0007910757689 0.6916378212 109.7235761
0.01130695522 -0.722445605 -0.1151206103 218.7890856
0.7827360109 0.02247114902 -0.0331736979 16.50173145
0 0 0 1
2. as second step using tranformation matrix registering strcutre map to input image
flirt -in /usr/local/fsl/data/atlases/HarvardOxford/HarvardOxford-cort-maxprob-thr25-2mm.nii.gz -ref sE12001-0013-00001-000176-01.nii.gz -applyxfm -init atlastoimg.mat -o structuremp2img.nii.gz.
after the 2 steps i am not getting any errors but HarvardOxford-cort-maxprob-thr25-2mm.nii.gz and structuremp2img.nii.gz. are looking same when i viewed thru fsview.i am attching subject image
may be registration is not done ... can you please help me to solve this isssue..
help is appreciated
Thanks in Advance ..