We are starting a new study where we switched from a 8 to a 32 channels head coils and we observe that we are now having a very bad segmentation when using fsl first tool.

-One of our main question is about the reference brain templates that are currently available in fsl (we are using fsl 4.1.4), are they all 8 channels based images?
-If so, does fsl have a 32 channels based reference template that they can provide to us?
-If not, do you have any suggestion to improve our segmentation, I have tried manual segmentation and then use the -intref function, but I finally obtained the same results!

Thanks

Pascal Tetreault