[Vv] Subtracting a preset value from the image & thresholding query

[Bilal Tahir]

Dear Rômulo,

Thanks for your help. The binarize option does what I need. However, I
think there may be a bug. This is because whenever I binarize my lung MRI
data, it changes the orientation of the output image. I.e. it displays a
coronal slice where it should display an axial (checked by clicking on F4)
and an axial slice where it should be displaying a coronal slice.

I checked this both for the original raw Dicom data and converted
.mhd metaimage. I had a look at the parameters of each image and all of
them stay the same (e.g pixel size, spacing, origin etc.) except for the
transformation matrix. As you can see below the transformation matrix
changes from:
[image: Inline images 1]

to the below matrix for the binarized image:

[image: Inline images 2]

I need to use the binarized image as the the moving image in Elastix
registration software. My fixed image which is CT is the same orientation
as the non binarized imaged. I suspect this may cause problems with the
registration as I have encountered problems like this before, where the
coronal slice of the moving image is registered to an axial slice of the
fixed image. Please let me know if you can help.

Best wishes,

Bilal


On 13 February 2013 12:40, Rômulo Pinho <romulo.pinho at lyon.unicancer.fr>wrote:

>  Hello, Bilal,
>
> It seems you've found a (rare! :-p) bug in VV! Sorry for that... Please
> find an update at
>
> http://git.creatis.insa-lyon.fr/pubgit/?p=clitk.git;a=commitdiff;h=2ed633c7b7068441ef25d006934566e5369e4299
>
>
> As for the thresholding, maybe you've seen the Binarize option under the
> Tools menu item. It does nearly what you want, except that you can't really
> control the standard deviation... You basically set up the range of values
> that you wish to threshold, click OK, and a new image with the result is
> generated, which you can save afterwards.
>
> If you want to know the SD of the image (and other stats), I suggest you
> try the clitkImageStatistics tool, which is also part of the VV suite. Than
> you can do your own calculations and find the range for the thresholnding.
> As a side note, you can also use the clitkBinarizeImage tool for the
> thresolding.
>
> Let us know if you any issues.
>
> Cheers,
> Rômulo
>
> --
> Rômulo PINHO
> Post-doc Assistant Researcher
> Centre Léon Bérard
> 28, rue Laennec 69373
> Lyon, France +33 (0)4 78 78 51 50 romulo.pinho at lyon.unicancer.fr http://www.creatis.insa-lyon.fr/rio/RomuloPinho
>
>
>  On 02/13/2013 02:17 AM, Bilal Tahir wrote:
>
> Dear All,
>
>  In tools > Image arithm there are a number of operations that can be
> performed on a single image. However, there doesn't seem to be an option to
> subtract a value from the image data - only addition is present.
>
>  I want to subtract 1 from each pixel in my image.
>
>  In the Sum A(x) + v option I try to set the value as -1 but it doesn't
> allow me to set a negative value? Is there an option to do it in vv?
>
>  Furthermore, I would like to know if vv allows for thresholding of image
> data. E.g. I would like to set all values above a certain value to zero
> e.g. Say I want to set all values of pixels above 1 standard deviation to
> zero but at the same keep the pixel values for those below this threshold,
> is there a way this can be done within vv?
>
>  If not, is there any software that can do this easily for .mhd
> metaimage/DICOM files without needing to convert them into MATLAB and
> convert them back?
>
>  Best wishes,
>
> Bilal Tahir,
> James Morrison Researcher in Radiotherapy Imaging
>
>
>
> _______________________________________________
> vv mailing list
> vv at creatis.insa-lyon.fr
> http://www.creatis.insa-lyon.fr/mailman/listinfo/vv
>
>


-- 
Bilal Tahir,
James Morrison Researcher in Radiotherapy Imaging
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