[slicer-users] visible hman project

Steve Pieper pieper at bwh.harvard.edu
Mon Dec 13 14:48:03 EST 2010


yes - that's the info you need about the spacing.

For saving, just select the color image volume and set the type to be 
.nrrd and then run the command I sent earlier.  then you can reload the 
grayscale volume.

-Steve

On 12/13/2010 02:38 PM, H B wrote:
> 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 t he 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
>  > > >
>  > > & gt; 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.
>  > > > > >
>  > > > > & gt; 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
>  > > > & gt; >
>  > > > > >
>  > > > > > 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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>  > >
>  > >
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