[Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data

Thu Nov 20 18:40:20 EST 2014

Dear Chao,
thanks very much for your help.
I will try this command now. Result will be given later.
Thanks again for your generous help and valuable time.
Another question is , how to visual the large volume effectively?? 3D
slicer is okay to handle this??
BTW， as for the xtekct  file, file attached  is the geometry of Nikon H225
in the lab .
[image: 内嵌图片 1]

Best  regards /谢谢您！
Guangming.
*Guangming Zang (Alex)*
*King Abdullah University of Science and Technology(KAUST)*
*University of Chinese Academy of Sciences(UCAS)*

2014-11-21 2:14 GMT+03:00 Chao Wu <wuchao04 at gmail.com>:

> Without more details I can only guess the meanings in your device xtekct
> file... suppose that the unit is mm.
>
> Before anything, first check the resolution of your tiff files and see if
> it is 200 dpi.
>
> Then try these geometry settings:
>
> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360
> --sdd=983 --sid=618.327880859375  --proj_iso_x=-121.666 --proj_iso_y=-97.536
> or
> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360
> --sdd=983 --sid=618.327880859375  --proj_iso_x=-121.666 --proj_iso_y=-97.536
>
> Then for reconstruction:
>
> rtksart -g My_geo2.xml   -f  CudaRayCast  -b   CudaVoxelBased   -t 1  -p
> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha  -n 3
> --spacing=0.08  --dimension=1800,900,1800
>
> No idea if these will work though...
>
> Best regards,
> Chao
>
>
> 2014-11-20 20:28 GMT+01:00 Guangming Zang <guangming.zang at kaust.edu.sa>:
>
>>  Hi Cyril,
>>
>> It is so nice of you, thanks for your very helpful help and reply.  And
>> thanks for introduction  about the visualization tool ( VV ) . Yes,
>> actually, i want to use SART to reconstruct a whole volume. Considering
>> that it may be kind of time-consuming, so i just try to reconstruct one
>> slice first.
>>
>> And I want to use sart reconstruction algorithm from a series of
>>  projections data scanned from Nikon  XT H 225 (.tif format,360
>> projections and 360 arcs) . But when using sart, I am not sure about the
>> geometry in our RTK setting.
>>
>> File attached(two files) are  the geometry information of object scanned
>> and 360 projections, I used the command below, but I can not get the
>> correct answer, I think it is because my geometry’ setting is not correct,
>> I used 2 commands:
>>
>> Command 1
>>
>> rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360
>> --sdd=983 --sid=618  --proj_iso_x=0 --proj_iso_y=-195
>>
>> command 2
>>
>> rtksart -g My_geo2.xml   -f  CudaRayCast  -b   CudaVoxelBased   -t 1  -p
>> C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha  -n 3
>> --spacing=0.08     --dimension 150 150 100
>>
>> In command 1, I am not sure about the proj_iso_x and proj_iso_y setting,
>> does it mean that the coordination of scanned object’s center map to the
>> projection? i used (0,-195) because in the geometry file (xml attached) the
>> object coordination is(0,192,633.82)    And the spacing setting as the
>> VoxelSize of x ,y,z. which is 0.07988 in xml.
>>
>> In command 2 , I am not sure about the dimension  and origin setting. I
>> setting dimension as dimension(x,y,z)= (VoxelSizeX*VoxelsX,
>> VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100)
>>
>> And in sart options , I do not know how to set origin in my case. So I
>> just use defult value, but I think in my case, I should change the value.
>>
>> in the xml file, i think maybe this may related to the origin setting
>>
>>    <VolumeOfInterest>
>>
>>     <XStart>21</XStart>
>>
>>     <XEnd>1757</XEnd>
>>
>>     <YStart>108</YStart>
>>
>>     <YEnd>1851</YEnd>
>>
>>     <ZStart>293</ZStart>
>>
>>     <ZEnd>1135</ZEnd>
>>
>>   </VolumeOfInterest>
>>
>> So can you help me to figure it out??
>>
>> And , another question is, if I want to resize the projections(e.g, from
>> 2000*2000 to 500*500. How should I change my geometry setting in this
>> case)???
>>
>> Again, thanks and very grateful for your any help and suggestion.
>>
>> I am not sure if you can see the attached file, so if you want, the 360
>> projections and geometry data are available at
>> https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing
>>
>>  The geometry only
>>
>>
>> https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing
>>
>>
>> Thanks for you all, Cyril ,Simon and Chao
>>
>>
>> Best regards
>>
>> Guangming
>>
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>

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