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<div class="moz-cite-prefix">Hello, Bilal,<br>
<br>
I was just starting to reply to your previous message...<br>
<br>
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.<br>
<br>
Best,<br>
Rômulo<br>
<br>
On 02/13/2013 10:41 PM, Bilal Tahir wrote:<br>
</div>
<blockquote
cite="mid:CAFZ9P6EXQLnnaUQn4Wx6Ya2knYsdX9zJMVTPJ2euN4c1cjM-0w@mail.gmail.com"
type="cite">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 moz-do-not-send="true"
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:part2.09090209.06000900@lyon.unicancer.fr"
alt="Inline images 1">
<div><br>
</div>
<div>to the below matrix for the binarized image:</div>
<div><br>
</div>
<div><img
src="cid:part3.02060206.09010609@lyon.unicancer.fr"
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 moz-do-not-send="true"
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 moz-do-not-send="true" 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 moz-do-not-send="true" href="tel:%2B33%20%280%294%2078%2078%2051%2050" value="+33478785150" target="_blank">+33 (0)4 78 78 51 50</a>
<a moz-do-not-send="true" href="mailto:romulo.pinho@lyon.unicancer.fr" target="_blank">romulo.pinho@lyon.unicancer.fr</a>
<a moz-do-not-send="true" 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>
<br>
</div>
</div>
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target="_blank">vv@creatis.insa-lyon.fr</a><br>
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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>
</blockquote>
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