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Dear FSL Experts, I’ve acquired pilot subject data (Anatomical and Functional) in the oblique plane at 30 degrees above AC-PC to minimize signal dropout in frontal regions due to susceptibility differences. I realigned the data to the main structural highres image and standard MNI space, but it was way off even if I did full search. I looked at the data in fslview and the labels were off because the brain is tilted 30 degrees. Therefore, I decided to warp the data into the cardinal plane using AFNI’s 3dWarp and Tshift programs (functional) and the data labels were accurate in fslview. I have multiple runs, so I put each run into a separate first level analysis and then combined the feat files into a 2nd level analysis. When I looked at the sum of all input masks, I knew that something went wrong because the mask covers the whole square for each brain slice rather than just the brain. As far as I can tell the registration looks really good for each run. I’ve seen this problem before, but that was due to fsl not being able to understand the labels provided in the conversion program I was using so I know that’s not the problem here since the labels are accurate. Just to see what would happen, I ran the oblique data through the whole processing stream and the sum of all masks looks right, but the registration is completely wrong. It seems like the 3dWarp program may be doing something to the data that’s creating this error. If anyone has any suggestions of how best to analyze oblique data in FSL, I would greatly appreciate it. I’ve looked it up, but I’m not finding too much. Also, this may be a related problem, but this is the first time I’ve analyze multiple runs in FSL and I notice that the brain activation for main effects (task vs baseline fixation) doesn’t always produce a lot of activation (not even in the visual cortex and this task has IAPS pictures). I’m wondering if this could be related to the problem I’m having here or if it may be a separate issue. Any insight into this issue would also be greatly appreciated. Many thanks, Dana