Hi, first of all thanks for your advices, it's really kind for you to share your experience!
I still have some further questions want to ask,
1. After I marked the structure manually, should I generate the weighting mask in flirt function, or should I use other function?
2. Are functional images use the same co-registration approach like you mentioned to the anatomical or to the standard space?
3. Is there any standard space for rat? I've downloaded the Waxholm space for SD rat, however i am not sure how can I use these data. Should I rescale the T2* image because of the really high resolution, or should I use the atlas file?
Here is the template I've downloaded : https://www.nitrc.org/projects/whs-sd-atlas
Thanks again for your help!!!
Best regards!
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