Hello, everyone,

I am a new FSL tool user. I am doing a longitudinal MRI study of volumetric changes of schizophrenic brains with Siena. The softwares you developed give me a lot of help.
But with BET threshold -f0.50, there are always some problems of overstripping on the top of the brains (along superior surfaces, although not very serious, but it might give difference because the presumable change on schizophrenic brain should be subtle) and non-brain tissues inferior to the brain (larynx, even mouth) left. My brain images are T1 weighted images sliced in coronal direction.

Is it a better way that I reslice the images into transverse direction and run BET at first by changing Threshold gradient? Or do I have to do manual correction to .seg files?

And in terms of the order of file A and B ( in command: siena A B), do I have to put the image with higher quality as the A, while the relatively poor one as B? I have checked both orders and got different PBVC results? Why is that?

By the way, my final aim is to get the volumetric changes on different parts of brains. Can you give me any advice about how to use the image files that can be got with Siena to go down to certain parts of brains? Can I use some digital atlas to accomplish this?

I will appreciate it if you could give me any suggestions in your convenience.

Best regards

Frank Sun



--
[log in to unmask]
--
[log in to unmask]