Slicer displays incorrect pixel values

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Slicer displays incorrect pixel values

Adam Blais-2
Hi all,

I have images which I have confirmed (using MATLAB) to be comprised of 16 bit integers. The actual pixels values are -1, 1 and 2 in the image. When I load them into Slicer, it display these values as -1, 256 and 512. The Volume Information section of the Volumes module says the Scalar Type is Short, and I'm not sure why.

I know there is something going on here with bit type but I don't know enough about Slicer to determine the problem.

Thanks,
Adam

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Re: Slicer displays incorrect pixel values

Julien Finet
Hi Adam,

Could you share with us your data ?

If you need a place to upload your data, you can consider MIDAS: http://slicer.kitware.com

Julien.



On Wed, Jan 16, 2013 at 11:37 AM, Adam Blais <[hidden email]> wrote:
Hi all,

I have images which I have confirmed (using MATLAB) to be comprised of 16 bit integers. The actual pixels values are -1, 1 and 2 in the image. When I load them into Slicer, it display these values as -1, 256 and 512. The Volume Information section of the Volumes module says the Scalar Type is Short, and I'm not sure why.

I know there is something going on here with bit type but I don't know enough about Slicer to determine the problem.

Thanks,
Adam

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Re: Slicer displays incorrect pixel values

Adam Blais-2
I'm not sure that it's a bug in Slicer, it may be a built-in, intended behaviour. I thought maybe it was a rescale slope issue, but my image (attached) doesn't have a header for that.


On Wed, Jan 16, 2013 at 11:59 AM, Julien Finet <[hidden email]> wrote:
Hi Adam,

Could you share with us your data ?

If you need a place to upload your data, you can consider MIDAS: http://slicer.kitware.com

Julien.



On Wed, Jan 16, 2013 at 11:37 AM, Adam Blais <[hidden email]> wrote:
Hi all,

I have images which I have confirmed (using MATLAB) to be comprised of 16 bit integers. The actual pixels values are -1, 1 and 2 in the image. When I load them into Slicer, it display these values as -1, 256 and 512. The Volume Information section of the Volumes module says the Scalar Type is Short, and I'm not sure why.

I know there is something going on here with bit type but I don't know enough about Slicer to determine the problem.

Thanks,
Adam

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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject



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im101.dcm (33K) Download Attachment
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Re: Slicer displays incorrect pixel values

Steve Pieper
According to dcmdump of that file, the data is signed 16 bit (PixelRepresentation of 1 means signed) so loading it as type short is correct.

The header does claim that the highest value is 2, but slicer says 512 and so does osirix -- probably there's an issue in the matlab export.

-Steve

(0028,0100) US 16                                       #   2, 1 BitsAllocated
(0028,0101) US 16                                       #   2, 1 BitsStored
(0028,0102) US 15                                       #   2, 1 HighBit
(0028,0103) US 1                                        #   2, 1 PixelRepresentation
(0028,0106) SS -1                                       #   2, 1 SmallestImagePixelValue
(0028,0107) SS 2                                        #   2, 1 LargestImagePixelValue


On Wed, Jan 16, 2013 at 12:13 PM, Adam Blais <[hidden email]> wrote:
I'm not sure that it's a bug in Slicer, it may be a built-in, intended behaviour. I thought maybe it was a rescale slope issue, but my image (attached) doesn't have a header for that.


On Wed, Jan 16, 2013 at 11:59 AM, Julien Finet <[hidden email]> wrote:
Hi Adam,

Could you share with us your data ?

If you need a place to upload your data, you can consider MIDAS: http://slicer.kitware.com

Julien.



On Wed, Jan 16, 2013 at 11:37 AM, Adam Blais <[hidden email]> wrote:
Hi all,

I have images which I have confirmed (using MATLAB) to be comprised of 16 bit integers. The actual pixels values are -1, 1 and 2 in the image. When I load them into Slicer, it display these values as -1, 256 and 512. The Volume Information section of the Volumes module says the Scalar Type is Short, and I'm not sure why.

I know there is something going on here with bit type but I don't know enough about Slicer to determine the problem.

Thanks,
Adam

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject



_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


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To unsubscribe: send email to [hidden email] with unsubscribe as the subject