[Vv] Subtracting a preset value from the image & thresholding query
romulo pinho
romulo.pinho at lyon.unicancer.fr
Wed Feb 13 22:56:01 CET 2013
Hello, Bilal,
I was just starting to reply to your previous message...
You are right, but in principle it is more like a feature than a bug,
i.e., we don't copy matrix information to the result of an operation.
We'll discuss this internally and decide if we'll update it or not. For
now, please stick with the solution you've found. We'll keep you posted.
Best,
Rômulo
On 02/13/2013 10:41 PM, Bilal Tahir wrote:
> 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
> <mailto: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:
> Inline images 1
>
> to the below matrix for the binarized 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
> <mailto: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 <tel:%2B33%20%280%294%2078%2078%2051%2050>
> romulo.pinho at lyon.unicancer.fr <mailto: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
>
>
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>
>
>
>
> --
> Bilal Tahir,
> James Morrison Researcher in Radiotherapy Imaging
>
>
>
>
> --
> Bilal Tahir,
> James Morrison Researcher in Radiotherapy Imaging
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