Dear Mark and Steve,
Thank you for your replies. I've checked my mask in standard space and it looks reasonable. I've used fslreorient2std on it and it didn't make any changes to my mask. I've tried the registration again but without any success.
The reason why I'm suspecting that there is something wrong with the transformation matrix (I2std_inv.mat) is that when I try to realign any of FSL standard masks it doesn't work properly. As i mentioned before I was quite surprised to see this since SIENAX segmentation worked fine. Is there a way to check if its a problem with the matrix?
cheers,
Lukasz
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