Dear All,<div><br></div><div>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. </div>
<div><br></div><div>Best wishes,</div><div><br></div><div>Bilal <br><br><div class="gmail_quote">On 13 February 2013 18:20, Bilal Tahir <span dir="ltr"><<a href="mailto:b.tahir@sheffield.ac.uk" target="_blank">b.tahir@sheffield.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><span style="font-family:Arial">Dear Rômulo,</span></div><div><span style="font-family:Arial"><br></span></div><div>
<span style="font-family:Arial">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. </span></div>
<div><span style="font-family:Arial"><br></span></div><div><font face="Arial">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:</font></div>
<img src="cid:ii_13cd4bbe5a86d7a5" alt="Inline images 1"><div><br></div><div>to the below matrix for the binarized image:</div><div><br></div><div><img src="cid:ii_13cd4bc94e794a24" alt="Inline images 2"><br></div><div><br>
</div><div>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.</div>
<div><br></div><div>Best wishes,</div><div><br></div><div>Bilal</div><div><br><br><div class="gmail_quote"><div><div class="h5">On 13 February 2013 12:40, Rômulo Pinho <span dir="ltr"><<a href="mailto:romulo.pinho@lyon.unicancer.fr" target="_blank">romulo.pinho@lyon.unicancer.fr</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
<div bgcolor="#FFFFFF" text="#000000">
<font size="-1"><font face="Arial">Hello, Bilal,<br>
<br>
It seems you've found a (rare! :-p) bug in VV! Sorry for that...
Please find an update at </font></font><br>
<pre><a href="http://git.creatis.insa-lyon.fr/pubgit/?p=clitk.git;a=commitdiff;h=2ed633c7b7068441ef25d006934566e5369e4299" target="_blank">http://git.creatis.insa-lyon.fr/pubgit/?p=clitk.git;a=commitdiff;h=2ed633c7b7068441ef25d006934566e5369e4299</a></pre>
<font size="-1"><font face="Arial"><br>
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.<br>
<br>
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.<br>
<br>
Let us know if you any issues.<br>
<br>
Cheers,<br>
Rômulo<span><font color="#888888"><br>
</font></span></font></font><span><font color="#888888"><br>
<pre cols="72">--
Rômulo PINHO
Post-doc Assistant Researcher
Centre Léon Bérard
28, rue Laennec 69373
Lyon, France
<a href="tel:%2B33%20%280%294%2078%2078%2051%2050" value="+33478785150" target="_blank">+33 (0)4 78 78 51 50</a>
<a href="mailto:romulo.pinho@lyon.unicancer.fr" target="_blank">romulo.pinho@lyon.unicancer.fr</a>
<a href="http://www.creatis.insa-lyon.fr/rio/RomuloPinho" target="_blank">http://www.creatis.insa-lyon.fr/rio/RomuloPinho</a>
</pre></font></span><div><div>
<font size="-1"><font face="Arial"><br>
</font></font>
<div>On 02/13/2013 02:17 AM, Bilal Tahir
wrote:<br>
</div>
<blockquote type="cite">Dear All,
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>I want to subtract 1 from each pixel in my image. </div>
<div><br>
</div>
<div>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? </div>
<div><br>
</div>
<div>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?</div>
<div><br>
</div>
<div>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?</div>
<div><br>
</div>
<div>Best wishes,</div>
<div> </div>
<div>Bilal Tahir,
<div>James Morrison Researcher in Radiotherapy Imaging</div>
</div>
</blockquote>
<br>
</div></div></div>
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<br></blockquote></div><span class="HOEnZb"><font color="#888888"><br><br clear="all"><div><br></div>-- <br></font></span><div class="im">Bilal Tahir,<div>James Morrison Researcher in Radiotherapy Imaging</div>
</div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>Bilal Tahir,<div>James Morrison Researcher in Radiotherapy Imaging</div>
</div>