Hi Mark,
Thank you for the suggestion. I am wondering if I am running it correctly though.
I ran fslorient2std and robustfov on the T1 image with the following command and output:
fslreorient2std D001_3D_A
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
robustfov -i D001_3D_A
Final FOV is:
0.000000 180.000000 0.000000 240.000000 69.000000 170.000000
Both processes took only a few seconds to be completed. Is this normal?
Also, the BET is still showing a lot of neck. I have uploaded the screenshot on Dropbox at https://www.dropbox.com/s/2ud4rup1tiyjiu0/Screenshot%202014-01-23%2009.55.20.png
Having looked at all of the data, this error seems rather consistent. Inclusion of brain looks generally okay, but most of the errors concern the inclusion of the neck.
I was reading up about the fsl_anat script which includes bias correction amongst other processing techniques. Should I run my images through this pipeline before going to SIENA?
Many thanks for your help!
Best Wishes,
Elijah
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