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1. I am not sure what’s the weighting mask used for? 2. In our case, we set some tags on the T2 images for each rat, and co-registrate into the standard space, then you can apply the transform function just created on the functional images. 3. As I known, there is no standard space for rat. In our lab, we made one rat anatomical image as standard. We also co-registrate the standard image into rat atlas. So that we can apply the atlas directly into the image. I guess you can either use your T2* image or the Waxholm space for SD rat, as long as you can make your data co-registrated well. > On May 20, 2017, at 1:40 AM, Ting Chun Lin <[log in to unmask]> wrote: > > 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!