Hi Sasha,
If you use tkmedit to visualize the results, then the contrast change you
saw may be just due to the display problem (not exactly a problem) of
tkmedit.
You can move the mouse around the image to actually see whether the image
intensity values were changed or not.
I used mri_watershed a lot, and never saw it changed the original image
intensity (in the brain region).
But tkmedit will adjust its display contrast according to the dynamic
range of the original image. So once skull is removed, the max and min
intensity values of the image are very likely to be different, and the
image will then look differently in tkmedit.
-Xiao
On Fri, 19 Aug 2005, florent segonne wrote:
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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