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

Fri Nov 21 08:08:17 CET 2014

or scale you sdd by 2/3.

Regards, Chao
Sent from Samsung Galaxy Note 3
2014年11月21日 12:49 AM于 "Guangming Zang" <guangming.zang at kaust.edu.sa>写道：

> Hi Chao,
> I checked the tif file and just found the file information like this:
> Horizontal resolution 300 dpi
> Vertical resolution   300 dpi
> dimensions      1916*1536
> bit depth             16
>
> So it means that before the reconstruction, i should use some tool to
> convert the projections images from 300dpi to 200dpi???
> Best
> Guangming
>
> *Guangming Zang (Alex)*
> *King Abdullah University of Science and Technology(KAUST)*
> *University of Chinese Academy of Sciences(UCAS)*
>
>
> 2014-11-21 2:40 GMT+03:00 Guangming Zang <guangming.zang at kaust.edu.sa>:
>
>> 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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