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

[Bilal Tahir]

Dear All,

I have found a solution to the problem I encountered which may be of some
interest to you. Basically if you copy the information in the .mhd header
of the non-binarized .raw image into the binarized one it works.

Best wishes,

Bilal

On 13 February 2013 18:20, Bilal Tahir <b.tahir at sheffield.ac.uk> wrote:

> 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
>



-- 
Bilal Tahir,
James Morrison Researcher in Radiotherapy Imaging
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.creatis.insa-lyon.fr/pipermail/vv/attachments/20130213/614093a5/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 2872 bytes
Desc: not available
URL: <http://www.creatis.insa-lyon.fr/pipermail/vv/attachments/20130213/614093a5/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 3599 bytes
Desc: not available
URL: <http://www.creatis.insa-lyon.fr/pipermail/vv/attachments/20130213/614093a5/attachment-0001.png>