[Rtk-users] Fwd: some bugs in SART when running Reconstruction of Elekta Data
Guangming Zang
guangming.zang at kaust.edu.sa
Thu Nov 20 18:49:01 EST 2014
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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