Processing 2D Tiff CT images...

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Processing 2D Tiff CT images...

mitchcud
Hi,

Just wondering if I'm anyone can tell me where I'm going wrong here. I'm new to image processing etc., so go easy on me!

I'm trying to reconstruct a prosthetic tooth (made of ceramic) from CT slices, in order to ultimately create a 3D FE model. Now I've worked through some good tutorials (eg. http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial.html) but I seem to be stumbling somewhere along the way.

I'm loading TIFF files, which may be a problem but I'm not sure. I can add the files via the Add Volume option, and I can play around with Thresholding etc. but when I try and load the scene again to create the 3D surface model Slicer tells me that I'm working with empty datasets.

Any ideas would be greatly appreciated!

Thanks

Mitch
Mitch Cuddihy

Department of Civil Engineering
National University of Ireland (Cork)
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Re: Processing 2D Tiff CT images...

inorton
Hi Mitch,
Try saving your data in nrrd format. In the "Save" window, change the format to nrrd - but, if you have multiple series, make sure each volume has a different name so that they aren't overwritten. nrrd should be very reliable for re-opening scenes.
HTH,
-Isaiah

On Thu, Mar 10, 2011 at 10:55 AM, mitchcud <[hidden email]> wrote:
Hi,

Just wondering if I'm anyone can tell me where I'm going wrong here. I'm new
to image processing etc., so go easy on me!

I'm trying to reconstruct a prosthetic tooth (made of ceramic) from CT
slices, in order to ultimately create a 3D FE model. Now I've worked through
some good tutorials (eg.
http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial.html) but I seem to
be stumbling somewhere along the way.

I'm loading TIFF files, which may be a problem but I'm not sure. I can add
the files via the Add Volume option, and I can play around with Thresholding
etc. but when I try and load the scene again to create the 3D surface model
Slicer tells me that I'm working with empty datasets.

Any ideas would be greatly appreciated!

Thanks

Mitch

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Re: Processing 2D Tiff CT images...

mitchcud
Okay, I can do that.

But still even if I do that, when I try and use the Model Maker it seems to fail and looking at each slice it says:
"Lb: Out of Frame"
"Bg: Out of Frame"

Again, I'm a total beginner at image processing so if anyone could shed any light on this it would make my day!
Mitch Cuddihy

Department of Civil Engineering
National University of Ireland (Cork)
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Re: Processing 2D Tiff CT images...

Aucoin, Nicole
In the Model Maker there's a Debug flag under the Debug section, try
running it with that to see what the full output of the process is (look
in the Error Log window). You do need to set the output Models before
running it. See here for more documentation:
http://www.slicer.org/slicerWiki/index.php/Modules:ModelMaker-Documentation-3.6
The slice windows can have the volume recentred by using the Fit to
Window button, the Model Maker output isn't a volume though.

Nicole

mitchcud wrote:

> Okay, I can do that.
>
> But still even if I do that, when I try and use the Model Maker it seems to
> fail and looking at each slice it says:
> "Lb: Out of Frame"
> "Bg: Out of Frame"
>
> Again, I'm a total beginner at image processing so if anyone could shed any
> light on this it would make my day!
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/Processing-2D-Tiff-CT-images-tp2660888p2664627.html
> Sent from the slicer-users mailing list archive at Nabble.com.
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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>  

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Re: Processing 2D Tiff CT images...

mitchcud
Now my last question is: Can you process TIFF files at all?

All the documentation seems to suggest to me that the files need to be DCM...

thanks,
Mitch
Mitch Cuddihy

Department of Civil Engineering
National University of Ireland (Cork)
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Re: Processing 2D Tiff CT images...

Steve Pieper
In general tiff should work, yes (like .jpg or .png) as long as you
convert to single component.   But there won't be any pixel or slice
spacing information.  For that you need to edit the values in the
Volumes->Info pane to whatever the physical values are.

-Steve

On Mon, Mar 14, 2011 at 12:15 PM, mitchcud <[hidden email]> wrote:

> Now my last question is: Can you process TIFF files at all?
>
> All the documentation seems to suggest to me that the files need to be
> DCM...
>
> thanks,
> Mitch
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/Processing-2D-Tiff-CT-images-tp2660888p2676505.html
> Sent from the slicer-users mailing list archive at Nabble.com.
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Re: Processing 2D Tiff CT images...

mitchcud
Thanks Steve, but what exactly do you mean by "convert to single component"?

Mitch
Mitch Cuddihy

Department of Civil Engineering
National University of Ireland (Cork)
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Re: Processing 2D Tiff CT images...

Curtis Lisle
Hi Mitch,

I believe Steve was referring to making the image a grayscale (single component per pixel) instead of a color image (three components per pixel).  Many of the algorithms in Slicer are expecting single component images.  ImageMagick tools, like convert can autoprocess a stack of TIFFs to convert from color to grayscale, if this is necessary for your data.   As you've found, Slicer can read all the files in a single directory in as a single volume.  However, very little is known about the volume since there was no metadata.

Please forgive me, if this is review, but the measurements, such as pixel size in each of the 2 dimensions, and the spacing in the third dimension between the slices, should be added using Slicer's Volume Module tab before making a label map.  The label map process of masking what regions of the images are inside your model, can be done by hand in Slicer's editor or by running one of Slicer's Segmentation algorithms.  You might want to try the GrowCut algorithm in the Editor, the Robust Statistics Segmentation, or the Fast Marching Segmentation to make your label map.    

Once a labelmap is constructed, it will have the dimensions extracted from the metadata added in the Volume Module.  Then running the ModelMaker should create a model.  

If you are using the Grayscale ModelMaker instead to run directly off your source imagery, eliminating the explicit labelmap step, you should be able to do this once your original imagery is single component.  

I know these comments are a bit sparse, but I hope it helps and makes sense when you take it along with the openpaleo tutorials you have been through.  Slicer's own tutorials offer good guidance on how to repeat this process, as well.  

Curtis

 
On Mar 16, 2011, at 1:23 PM, mitchcud wrote:

> Thanks Steve, but what exactly do you mean by "convert to single component"?
>
> Mitch
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/Processing-2D-Tiff-CT-images-tp2660888p2688721.html
> Sent from the slicer-users mailing list archive at Nabble.com.
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Re: Processing 2D Tiff CT images...

Steve Pieper
In reply to this post by mitchcud
Hi Mitch -

By "convert to single component" I meant this step:
If you have saved your volume in nrrd format as Isaiah suggested, say
as /tmp/imRGB.nrrd, you can use this command to convert it:

unu project -a 0 -i /tmp/imRGB.nrrd -o /tmp/imGRAY.nrrd -m mean

Best,
Steve

On Wed, Mar 16, 2011 at 1:23 PM, mitchcud <[hidden email]> wrote:
> Thanks Steve, but what exactly do you mean by "convert to single component"?
>
> Mitch
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/Processing-2D-Tiff-CT-images-tp2660888p2688721.html
> Sent from the slicer-users mailing list archive at Nabble.com.
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