I've just started using fsl and I currently have coronally acquired images
that have been converted from dicom to analyze using mricro (256 124 256).
The BET function appears to include alot of non-brain. I have tried to tune
the parameters and change the image centre as suggested in previous emails.
However I still get non-brain tissue in the extracted image. I want to do
serial atrophy measure using siena and don't know how this will affect the
output measure. I was thinking of manually editing the bet images and then
running the siena script. Is this possible? if so which images from bet do
I need to edit and which lines in the siena script do I need to comment out?
I presume to run the siena script I enter the extracted edited image
filenames as input1 and input2?
I hope someone can help.