Dear FSL Experts,
I am working on fMRI data collected with a reduced FOV (24 slices, 3.5 mm each), multiband factor of 6 and TR of 265ms. I have collected a structural scan and five functional 4D images from 5 sessions of the experiment. Now I am using FLIRT to register those functional images to standard space. But the problem is, that the results from those registrations are very poor. I am attaching one example with this mail. It's an extreme case where both translation and rotation are completely wrong but in 90% of them, there is orientation issue, where the bottom edge of the reduced-FOV-image has been matched with the bottom edge of the standard image.
My workflow goes as follows:
Say, I have run1.nii, run2.nii, and so on and their corresponding high contrast reduced FOV reference images SBRefs i.e. run1_SBRef.nii, run2_SBRef.nii and so on. And I also have a structural scan i.e. structural.nii. First, I register run1.nii to run1_SBRef.nii and then to structural_brain.nii (brain image extracted from structured.nii) and then to standard space.
Now, I am going to try a few options in FLIRT but it will be great if you could guide me in the right direction.
Thanks alot,
Usman Ayub Sh,
PhD Researcher @ BCBL
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