hello, everyone
I want to register the diffusion image of rat brain to standard image. But when I registered its structural image(T2 image) into a standard image, I got a bad result. The attachment shows the results explicitly. I want to if something I have done wrongly.
The command I used is "fnirt --ref=standard.nii.gz --in=msme_enlarge10.nii --aff=msme2standard.mat --cout=msme2standard_warp --iout=msme2standard_fnirt --jout=msme2standard_jac --warpres=10,10,10"
(’msme_enlarge10.nii’ is T2 image of the rat brain, and the T2 image has been enlarged 10 times compared with the original raw data)
By the way, both T2 image and standard image have no skull. Because the data was collected in vitro, I didn't have the data with skull. I don't know if the bad result was caused because of the T2 image without skull. If exactly so, are there any advice for registering diffusion image into standard image when the T2 image has been skull-striped.
I will appreciate so much for your help.
Best,
Zhaoqing
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