thank you for your suggestions.
I have also tried to run fsl FLIRT outside of fsl_anat and also running without crop
I get the same registration errors.
It may be BET. It didn't remove non-brain area near the neck. I did go in and try to remove as much of this with the manual cropping feature in fsleye and tried to rerun the registration to MNI. This also resulted in the registration failing. I wasn't able to removed all of the non-brain area though. This was because the cropping function was a square and if I removed the bottom too much, then I also ended up removing cerebellum. Any suggestions on how to do this better would be greatly appreciated.
Also, the brain was very low in the FOV. I tried to crop this so that it would remove some of the dead space at the top. This also did not fix the registration errors.
I am attaching a visual of the original T1.
Also, I should state, the registration errors happened on two T1 images. These were of the same subject and the above issues were on both of the BET scans, but nevertheless, happened on two separate T1 scans.
Please Help :(
Jen
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