Alternatively, depending on what version of tkmedit you have, you can use the -mm-main <min> <max> option to specify an out-of-range min and max visible value on the command line. As Xiao said, normally the min and max visible values that determine the color scale are preset to the actual min and max values in the volume. In the View->Configure->Brightness / Constrast dialog box, you cannot specify values outside of this range. However, if on the command, you do:

tkmedit bert T1 -mm-main 0 500

This will set the min and max visible values to 0 and 500, even though 500 is above the max value in the volume.

Note that your version of tkmedit may not have this option, so if you get an error when trying this, ignore this email. :)

On Fri, 19 Aug 2005, Xiao Han wrote:

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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