[Rtk-users] scanner development problems

Simon Rit simon.rit at creatis.insa-lyon.fr
Mon Mar 21 11:46:55 EDT 2016


Hi,
It seems to me that your window/level is not adjusted for visualization 
which is not an RTK problem. What software do you use for visualization? 
Try to find out how to adjust the contrast on it. I can't see from the 
image you sent if there is a problem and what it is.
Regarding rings, I'm not sure it comes from the calibration, these are 
probably due to defects in your projections. A simple solution is to 
pass a median filter, e.g., with rtkmedian.
Simon

On 21/03/2016 15:25, Vasiliy Nabokov wrote:
> It worked now. The phantom artifact was caused by wrong rotate 
> direction xD So, when i changed sort of regex result of my tifs from 
> asc to desc phantom was disappeared!
> After scanner geometry calibration by article above, and my self 
> algorithms i got not bad reconstruction by RTK for me. But there still 
> remain two problems..
> Here is one slice http://i.imgur.com/oVHCodb.png reconstructed from 
> scans like this http://i.imgur.com/qIYkvY7.png
> 1). Contrast. Structure reconstructs good, but hard to see. I receive 
> 12 bit per pixel raw data from the detector, convert it to 16 bit just 
> by (/4095.)*65535. What options i should play in RTK or while tifs 
> generation at acquisition process in order to make structure more 
> visible ? I tried different variants of voltage and current of tube, 
> but on the picture is the best variant of contrast...
> 2). Also on the slice you can see circles that come from center. As i 
> think its still geometry problems, i have to do calibration process 
> better, isn't it ?
>
>
>
> On Fri, Mar 18, 2016 at 1:27 PM, Simon Rit 
> <simon.rit at creatis.insa-lyon.fr 
> <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>     Ok, sorry, I erroneously mixed the size of the reconstructed
>     volume and the size of the projections. Then your calculation
>     seems correct and I don't know where does your geometry problem
>     come from. For sure, you don't have to shift the projections,
>     --proj_iso_x does the same thing directly.
>     Regards,
>     Simon
>
>     On Thu, Mar 17, 2016 at 4:23 AM, Vasiliy Nabokov
>     <nabokajeleboka at gmail.com <mailto:nabokajeleboka at gmail.com>> wrote:
>
>         Dear Simon, as i understand --neworigin is origin for
>         projections. my projection's width 2452 and spacing 0.0148, so
>         2451/-2*0.0148=-18.137
>
>         On Wed, Mar 16, 2016 at 6:45 PM, Simon Rit
>         <simon.rit at creatis.insa-lyon.fr
>         <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>             Hi,
>             I think it's a geometry problem. I don't have a solution
>             for you but just a remark: how did you come up with the
>             neworigin parameter? Changing this has a similar effect as
>             changing the --proj_iso_x or "offseting" the projections.
>             And it seems that the value you put (-18.137) makes no
>             sense to me wrt the total width (800*0.0296=23.68).
>             Typically, I center the projection which in your case
>             would require as a new origin 799/-2*0.0296.
>             I hope this helps,
>             Simon
>
>             On Wed, Mar 16, 2016 at 1:11 PM, Vasiliy Nabokov
>             <nabokajeleboka at gmail.com
>             <mailto:nabokajeleboka at gmail.com>> wrote:
>
>                 Hi dear RTK users. Sorry, its offtop post... i just
>                 wanna tell you about my problems if anyone can help me..
>                 I develop scanner. Reconstruction of parallelepiped or
>                 cube (http://i.imgur.com/9YHyfWH.jpg) caused to
>                 phantom artifact (http://i.imgur.com/yyI184j.png).
>                 Don't look at noise, its test scan, without averaging
>                 and big rotation step.  Yea, it seems that its mainly
>                 misalignments problems, so i calibrated sourceX,
>                 sourceY, detectorX, detectorY by the following method
>                 http://www1.jinr.ru/Pepan_letters/panl_2015_5/10_gongad.pdf,
>                 got sourceX = -215 mkm, sourceY = 650 mkm, detectorX =
>                 50mkm. i specify this information but without success.
>
>                 I also wrote a little program in this way
>                     for (float sourceXOffset_ = sourceXFrom;
>                 sourceXOffset_ < sourceXTo; sourceXOffset_ += searchStep)
>                     for (float sourceYOffset_ = sourceYFrom;
>                 sourceYOffset_ < sourceYTo; sourceYOffset_ += searchStep)
>                     for (float projXOffset = projXFrom; projXOffset <
>                 projXTo; projXOffset += searchStep)
>                     {
>                         sprintf(cmd, "./rtksimulatedgeometry -o
>                 geometry.xml --n 90 --arc=360 --sdd=232.241 --sid=170
>                 --source_x=%.6f --source_y=%.6f --proj_iso_x=%.6f",
>                 sourceXOffset_, sourceYOffset_, projXOffset);
>
>                         int r = system(cmd);
>
>                         sprintf(cmd, "./rtkfdk --hardware=cuda -p
>                 /home/fee/Public/ -r [0-9]+.tif$ -o dump/out.mha -g
>                 geometry.xml --verbose --dimension 800,1,800 --spacing
>                 0.0296 --newspacing 0.0148 --neworigin
>                 -18.137,-12.128,0 --subsetsize=1 -l --origin
>                 -11.8252,-3.55,-11.8252");
>                         r = system(cmd);
>                 ...
>
>                 to search scanner alignment but also without success.
>
>                 I noticed interesting thing: when i specially offset
>                 detector horizontally to the right by 4.5mm from the
>                 center, and specify it by --proj_iso_x=4.5 when
>                 generating geometry file, phantom disappears!
>                 (http://i.imgur.com/OOsPsfL.png) I even take scans
>                 when the detector on the center, reconstruct it, and
>                 here is phantom artifact, then i manually offset
>                 picture to the left on the tifs (from
>                 http://i.imgur.com/FGxCJUo.png to
>                 http://i.imgur.com/brbp5sd.png), and it reconstructs
>                 without phantom with --proj_iso_x=4.5! So, for this
>                 moment i work in this way, take scans when detector on
>                 the center, manually offset picture to the left and
>                 specify it by proj_iso_x to avoid phantom artifact,
>                 but its HUGE WORKAROUND =))
>
>
>                 What do you think about it ? If its geometry issue,
>                 why real or virtual offset of detector cleans up the
>                 phantom artifact?
>
>
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>
>
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