Date: Fri, 19 Aug 2005 14:25:48 -0400 From: "Sasha Wolosin" To: Subject: Re: [Freesurfer] mri_watershed Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Xiao, That seems to be it, thanks. The actual values are the same. I looked = at the brightness/contrast settings for the skull-stripped brain and = noticed that they had been automatically adjusted. So I matched the orig = volume brightness/contrast range to the brain brightness/contrast range, = and now they look identical- problem solved! Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 >>> Xiao Han 08/19/05 1:37 PM >>> Hi Sasha, If you use tkmedit to visualize the results, then the contrast change = you=20 saw may be just due to the display problem (not exactly a problem) of=20 tkmedit. You can move the mouse around the image to actually see whether the = image=20 intensity values were changed or not. I used mri_watershed a lot, and never saw it changed the original image=20 intensity (in the brain region). But tkmedit will adjust its display contrast according to the dynamic=20 range of the original image. So once skull is removed, the max and min=20 intensity values of the image are very likely to be different, and the=20 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=20 > preprocessing step, such as intensity normalization or contrast = modification.=20 > So, This certainly seems like a reasonable thing to do. > > However, mri_watershed might normalize intensities during the process = but=20 > should NOT generate skull-stripped images with different intensities. = We'll=20 > quickly look into this and let you know if this is a bug that needs to = be=20 > fixed. > > Cheers, > > Florent > > On Fri, 19 Aug 2005, Sasha Wolosin wrote: > >> We use an anatomical analysis program called Brain Image in our lab. = We=20 >> would like to speed up our analysis in Brain Image by replacing = manual=20 >> skull stripping with FreeSurfer's automated skull strip program. For = this=20 >> we would need to do a skull strip alone, without adjusting intensity = values=20 >> 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,=20 >> and the output volume looks much brighter than the orig volume. = Does=20 >> mri_watershed normalize intensities or change the contrast in order = to=20 >> strip the skull? >>=20 >> Thanks, >> Sasha >>=20 >> Sasha Wolosin >> Research Assistant >> Developmental Cognitive Neurology >> Kennedy Krieger Institute >> 707 N. Broadway >> Baltimore, MD 21205 >> ph: (443) 923-9270 >>=20 >>=20 >>=20 >> Disclaimer: >> The materials in this e-mail are private and may contain Protected = Health=20 >> Information. Please note that e-mail is not necessarily confidential = or=20 >> secure. Your use of e-mail constitutes your acknowledgment of these=20 >> confidentiality and security limitations. If you are not the intended=20= >> recipient, be advised that any unauthorized use, disclosure, copying,=20= >> distribution, or the taking of any action in reliance on the contents = of=20 >> this information is strictly prohibited. If you have received this = e-mail=20 >> in error, please immediately notify the sender via telephone or = return=20 >> e-mail. >>=20 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>=20 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >