Hi Sam
if you want us to help you, you need to provide us with the full
command line and screen output (at least!)
cheers
Bruce
On Tue, 21 Jul 2015, Sam Zorowitz
wrote:
Hi all,
I am using mri_watershed to create skull surfaces for a cohort of subjects
for whom we were unable to collect a FLASH sequence. To improve the
estimation of the inner skull layer, I would like to use edited brainmasks.
However whenever I supply the -mask flag, and only when I supply -mask flag
to mri_watershed, the code does not run; it only brings up the help screen.
So two questions:
(1) Is the -mask flag in mri_watershed doing what I think it is doing? Is it
masking the T1 image to only the brain so that the inner skull layer will be
estimated from the brainmask?
(2) Am I using the -mask flag correctly? I get the same result if I use
mri_watershed -mask and mri_watershed -mask <path to mask>. Should I be
doing something differently?
All the best,
Sam
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