Hi FSL experts,
I'm trying to realign several runs of a resting state dataset from the same subject (in rodents). There are some EPI susceptibility distortions due to the sinuses at the back of the brain, and these look different for the same subject over the different days, and therefore flirt is having a hard time realigning the images accurately. I am particularly interested in one, rather large, region. Is there some way to realign the runs with respect to this particular ROI?
Thank you so much for your help!
Annelene
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