[slicer-users] Help for making 3D view of brain MRI

Henkjan Huisman henkjan at m14-027.azn.nl
Thu Jun 21 03:26:32 EDT 2001


On Wed, 20 Jun 2001, Xu, Yanjun wrote:

> Hi, Lauren and slicer users,
>
> I got the 3D cut-trhough view. While I still has the following questions.
>
> 1. How can I get rid of the bounding-box display?
There's a module called Anno. Click on 'More:' ->Anno. Then press 3D Cube.
> 2. How can I get rid of the extracranial background display in each slice
> view?
In Volumes set threshold to remove these values.
> 3. The surface of the brain is unicolor. Can I put the real surface of brain
> as the texture of the model?
What do you mean by 'real' surface?
>
> Thanks a lot.
>
> Sincerely,
> Yanjun
>
> -----Original Message-----
> From: slicer at ai.mit.edu [mailto:slicer at ai.mit.edu]
> Sent: Monday, June 18, 2001 10:57 AM
> To: Xu, Yanjun
> Cc: 'slicer-users at bwh.harvard.edu'
> Subject: Re: [slicer-users] Help for making 3D view of brain MRI
>
>
> To make models such as the skin and brain in the tutorial, you can use
>
> two modules on the slicer menu: the Editor followed by the ModelMaker.
>
>
>
> The Editor module allows you to create a Working labelmap using editing
>
> operations such as Threshold and Draw.  This process is called
>
> segmentation.
>
>
>
> Once you have performed the segmentation the labelmap should have the
> brain marked in all one color.  Then you can click on the Make Model
> button under Editor->Effects.  Choose the Working labelmap on the
> Volume: menu, and choose the label you are interested in.  Then click
> Create.    The model should appear in the Viewer window.
>
> To display the cut-through, you will need to use the Clipping functions in
> the slicer.  First you can display the models and grayscale slices that
> you are interested in.  Then go to the Models->Display tab, and right
> click on the model that you want clipped.  This should be the skin model
> if you are using the tutorial data from the ftp site, for example.  A menu
> will appear, and you should choose Clipping to turn this on.
>
> Now the model will be cut by the grayscale slices.  Next go to the
> Models->Clip tab to adjust which side of each grayscale slice should be
> used to clip the model.
>
> And finally, to remove the black background in each of the grayscale
> slices, you may use thresholding.  Under the Volumes->Display tab there is
> a Threshold function.  Press the Auto button and the black background
> should disappear.  You may also manually adjust the thresholding to get
> the desired effect.
>
> Lauren
>
> On Mon, 18 Jun 2001, Xu, Yanjun wrote:
>
>
> > Hi, Dear slicer-users,
> >
> > I'm a beginner of 3D slicer. I wonder how to make a 3D view of brain MRI
> > like the picture in the Overview of the introduction. It should have both
> > the rendered brain surface and cut-through 3D view. I'd like to add some
> > colored statistical result if possible. Thanks a lot.
> >
> > Sincerely,
> > Yanjun
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-- 
Dear     ,


Yours,

Henkjan

---------------------------------------------------------------------
H.J. Huisman, PhD, MSEE       E : henkjan at radiology.azn.nl
Medical Imaging Scientist     T : +31 24 3617536/14545
Dept. Radiology               F : +31 24 3540866
UMC St. Radboud               S : 430 Radiologie/POBox 9101/
                                  6500HB Nijmegen/Netherlands






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