[slicer-users] visible hman project

H B r44cd at hotmail.com
Mon Dec 13 14:38:23 EST 2010


Hi Steve,
 
You realy help me.
When i was working in itk (converting to grayscale) i found this statement:
The original Visible Male cryosectional
// images are non-interlaced 24-bit RGB pixels with a resolution of
// 2048x1216 pixels by 1871 slices with a physical spacing of
// approximately 0.33 mm in slice and 1.0 mm between slices.
 
(the ftp which i download the dataset dose not contain information -readme.txt-) i will try to find any information through the web site
 
 
Q. When saving , it will save just one file beside mrml? or it should save as many as the dataset?
 
Thanks alot
 
H.B

 
> Date: Mon, 13 Dec 2010 14:14:51 -0500
> From: pieper at bwh.harvard.edu
> To: r44cd at hotmail.com
> CC: slicer-users at bwh.harvard.edu
> Subject: Re: [slicer-users] visible hman project
> 
> Hi -
> 
> On 12/13/2010 01:59 PM, H B wrote:
> > Hi Steve,
> >
> > How could i know pixel size of the oreginal image? it seems like stupid
> > question
> >
> 
> The pixel spacing is not in the image files for .jpg or .png - you 
> should be able to find it on the web page where you originally 
> downloaded the data.
> 
> > The Editor didnt work,and when i try to save it save the first image (i
> > choose nrrd).
> > When i try to open it it gave me error. Could you help? i dont know
> > where is the error in saving(may because it save the first png inly?)
> >
> 
> Be sure to pick the file type '.nrrd' when saving the data in slicer.
> 
> > About Lunix, untill now i call 3 maintenence shop but they didnt have
> > linux and they dont know how to download it. i will try tomorrow. (i
> > dont want to lose time in download it i have to find some shop to do it)
> >
> 
> A nice version of linux that is easy to install is available from 
> ubuntu.com. But if you are not familiar with linux you may be better 
> sticking with windows and sorting out the file format issues directly 
> (they will be the same on linux so they need to be fix one way or the 
> other).
> 
> Best of luck,
> Steve
> 
> > Regards,
> >
> > H.B
> >
> > > Date: Mon, 13 Dec 2010 13:30:30 -0500
> > > From: pieper at bwh.harvard.edu
> > > To: r44cd at hotmail.com
> > > Subject: Re: [slicer-users] visible hman project
> > >
> > > Hi -
> > >
> > > The spacing should be based on the input data - whatever is spec'd at
> > > the visibile human website. For example if the orignal pixel size was
> > > .1x.1 mm and the slices were 5mm thick, then if you resized the image
> > > files to 1/4 of their original size the spacing would be 4x4x5 (these
> > > are just made up numbers - you'll need to check.
> > >
> > > Best of luck,
> > > Steve
> > >
> > >
> > > On 12/13/2010 01:07 PM, H B wrote:
> > > > Hi steve,
> > > >
> > > > Thank you for your interest in my problem. I have write itk code to
> > > > convert it to grayscale. and i use resizing program as AF said.then it
> > > > opened but the editor didnt work with me, i am trying now to save it as
> > > > nrrd as you sa id.
> > > > what should i write when adjust the spacing?
> > > >
> > > >
> > > >
> > > > > Date: Mon, 13 Dec 2010 08:48:01 -0500
> > > > > From: pieper at bwh.harvard.edu
> > > > > To: r44cd at hotmail.com
> > > > > CC: slicer-users at bwh.harvard.edu
> > > > > Subject: Re: [slicer-users] visible hman project
> > > > >
> > > > > Hi H.B. -
> > > > >
> > > > > I think that worked for you - the only thing now is that the default
> > > > > window/level setting (contrast/brightness) don't look good for
> > the color
> > > > > images. You need to go to the Volumes->Display tab and adjust them.
> > > > > Also adjust the spacing to get the 3D proportions correct.
> > > > >
> > > > > Also, I'm not sure what your next plans are, but you should know that
> > > > > RGB color images like the visible human aren't supported in
> > slicer for
> > > > > much o ther than slice viewing. Many of the tools only work on
> > grayscale
> > > > > volumes.
> > > > >
> > > > > There's no GUI module in slicer to convert rgb to grayscale (probably
> > > > > there should be) but it's not hard to do by hand.
> > > > >
> > > > > First use File->Save to write out the color volume into a new
> > file (say
> > > > > 'savededcolor.nrrd' - be sure to set the file type to '.nrrd' in the
> > > > > save dialog).
> > > > >
> > > > > The bring up the Tcl Interactor (find it under the Window menu).
> > > > >
> > > > > In the console, enter this command:
> > > > >
> > > > > unu project -a 0 -m mean -i savedcolor.nrrd -o newgray.nrrd
> > > > >
> > > > > (you may need to add a path to where you saved the data -
> > something like
> > > > > c:/data/savedcolor.nrrd - be sure to use forward slashes, not
> > > > backslashes).
> > > > >
> > > > > Then load newgray.nrrd and adjust the window/level as needed.
> > > > >
> > > > > You will then be able to use the grayscale volume with the Editor and
> > > > > other slicer tools. If you create label maps, you can still
> > select the
> > > > > color image to use as the Bg layer in the slice windows.
> > > > >
> > > > > Best,
> > > > > Steve
> > > > >
> > > > >
> > > > > On 12/13/2010 01:16 AM, H B wrote:
> > > > > >
> > > > > >
> > > > > > >Hi all,
> > > > > >
> > > > > > now slicers can open the dataset, but it is black and white as
> > here:
> > > > > >
> > > >
> > http://www.alhnuf.com/up/pics-gif/upload/uploads/images/alhnufff98abcf15.jpg
> > > > > >
> > > > > > is there any thing should be done (set any value) in this case?
> > > > > >
> > > > > >
> > > > > > Regards,
> > > > > >
> > > > > > H.B
> > > > > >
> > > > > >
> > > > > >
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