I have previously run recon-all on a set of neuroimaging data (and as far as I can tell it ran successfully). I am now preparing to run FEAT preprocessing on fMRI data from the same group of subjects. I would like to use the skull-stripped output from freesurfer for registration in FEAT because it typically gives better results than BET.
When I open the freesurfer ouput (norm.nii.gz) in fsleyes the orientation labels are correct but the images display abnormally. This persists after I’ve run fsl-reorient2std. When I open the original image in the same window they align visually but I get a warning that the orientations are not aligned.
So what I am trying to figure out is:
- Can I fix the orientations so the freesurfer outputs display sensibly in FSLeyes
- If I can’t can I use the freesurfer files to align data in FEAT anyway?
- How do I get output from FSL aligned with output from freesurfer if these tools aren’t working.
I ultimately want to be able to use the anatomical region data from freesurfer as ROIs for resting state analyses so I do want to get these aligned eventually.
Thanks