Hello,
[EMAIL PROTECTED] doesn't seem to exist, so I'm
hoping one of you can help me out.
I seem to be having trouble with the -mask 0 flag in dtrecon. It doesn't apply
a brainmask! I tried -mask 1 but that didn't work either.
I unpacked the data properly, then ran
diff-flirt -i f -o unwarp/f -tmpdir tmp for motion and eddy current
correction and then ran dtrecon -i f -o maps -mask 0
but my maps/fa volume is not brain masked.
Here are the logs:
/space/thigpen/10/users/min/OFRR27/dti/025/unwarp/dtrecon-22259.log
/space/thigpen/10/users/min/OFRR27/dti/025/unwarp/raw2tensor-22289.log
/space/thigpen/10/users/min/OFRR27/dti/025/unwarp/tensor2eig-22447.log
I can see where it says
Calculating background fraction ...
brain is 100% of volume
nonbrain is 0% of volume
but I still don't understand why it's not working.
I even tried running dtrecon on the unpacked data without running diff-flirt,
but no luck.
Any and all help is highly appreciated.
Thanks!
Akram.
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