Dear Sasha,
mri_watershed was initially designed to skull strip orig images, without
any preprocessing step, such as intensity normalization or contrast
modification. So, This certainly seems like a reasonable thing to do.
However, mri_watershed might normalize intensities during the
process but should NOT generate skull-stripped images with different
intensities. We'll quickly look into this and let you know if this
is a bug that needs to be fixed.
Cheers,
Florent
On Fri, 19 Aug 2005, Sasha Wolosin wrote:
We use an anatomical analysis program called Brain Image in our lab. We would
like to speed up our analysis in Brain Image by replacing manual skull
stripping with FreeSurfer's automated skull strip program. For this we would
need to do a skull strip alone, without adjusting intensity values or contrast.
Is this possible? Is this a reasonable thing to do?
I have run mri_watershed with the input from orig on several subjects, and
the output volume looks much brighter than the orig volume. Does
mri_watershed normalize intensities or change the contrast in order to strip
the skull?
Thanks,
Sasha
Sasha Wolosin
Research Assistant
Developmental Cognitive Neurology
Kennedy Krieger Institute
707 N. Broadway
Baltimore, MD 21205
ph: (443) 923-9270
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