[Rtk-users] How to make the comparison?

[Guangming Zang]

Hi Chao,
Your explanation is very clear and helpful, thanks very much, Chao :)
As for the two ways  you suggested to generated a 128^3 size volume with
spacing =1, i prefer  the second one( i.e. first create a dimension=128 but
spacing=4 image file and subsequently change the spacing from 4 to 1.)
But the question is   after i first create a dimension=128 with spacing=4
image file, i got a output(That's say A.mha) . how could use the A.mha as a
input to generate a volume( B.mha) with spacing as 1? what command should i
use

BTW, Is it available to use RTK to generate SheppLogan phantom with
different volume size automatically ?
Thanks again.
Best regards
Guangming

*Guangming Zang (Alex)*
*King Abdullah University of Science and Technology(KAUST)*
*University of Chinese Academy of Sciences(UCAS)*




2015-05-11 14:18 GMT+03:00 Chao Wu <wuchao04 at gmail.com>:

> Hi Guangming,
>
> Glad to see you get it work.
>
> The size of the phantom is described in physical units (e.g. mm) in the
> txt file. The spacing of the image file is also in physical units (mm) and
> the dimension is in number of voxels. Therefore spacing * dimension gives
> you the physical size of the image volume. That's why if you want to have
> the same volume in mm^3 you need keep the spacing * dimension a constant.
>
> If you want to have a 128^3 dimension spacing=1 SheppLogan phantom with
> the *same* *content, not same physical size*, you are actually looking
> for a smaller phantom: 128 * 1 is 1/4 of 256 * 2, so it is 4 times smaller
> in length. You can get this phantom by changing the size description in the
> txt file, or you can first create a dimension=128 but spacing=4 image file
> and subsequently change the spacing from 4 to 1.
>
> Regards,
> Chao
>
> 2015-05-11 13:05 GMT+02:00 Guangming Zang <guangming.zang at kaust.edu.sa>:
>
>>
>>
>> Hi Chao,
>>
>> Thanks for your help.
>>
>> Yes, it works. But I am still a little confused.
>>
>>  In the example in wiki,
>> <http://wiki.openrtk.org/index.php/RTK/Examples/ADMMTVReconstruction>the
>> only input for  command rtkdrawgeometricphantom  is SheppLogan.txt, in
>> which , after I checked, the geometry information is not included. So I
>> thought I can generated any size of volume as I want. (for example, 64^3
>> volume dimension with spacing 1 or 1024^3 volume dimension with spacing 10)
>> why should  the   dimension *spacing (1*512=2*256=512)   should be fixed as
>> a  constant???
>>
>>
>> Briefly speaking,my question is , by using command rtkadmmtotalvariation
>> or rtkdrawgeometricphantom,
>> how can i generated a 128^3 dimension SheppLogan volume with spacing as 1
>> .  Is it possible for the SheppLogan.txt provided by this example  to make
>> it  ???
>>
>> So could you help me to find the solution??
>>
>> Thanks for your help, Chao.
>>
>> With my best regards
>>
>> Guangming
>>
>> *Guangming Zang (Alex)*
>> *King Abdullah University of Science and Technology(KAUST)*
>> *University of Chinese Academy of Sciences(UCAS)*
>>
>>
>>
>>
>> 2015-05-11 11:06 GMT+03:00 Chao Wu <wuchao04 at gmail.com>:
>>
>>> Hi Guangming,
>>>
>>> If you half the spacing you need twice the dimension (in length, or 8
>>> times in volume) to cover the same area, i.e. --spacing 1 --dimension 512.
>>> Is this what you want?
>>>
>>> Regards,
>>> Chao
>>>
>>> 2015-05-10 22:50 GMT+02:00 Guangming Zang <guangming.zang at kaust.edu.sa>:
>>>
>>>> Hi all.
>>>> I have implemented SART algorithm with some optimizations.and i wanna
>>>> to make a comparison with the implementations in our RTK.
>>>> My questions are:
>>>> 1. how to use RTK to  generate the initial  volume(i.e., ground Truth
>>>> )to make the comparison?
>>>> 2. My answer to the question 1 is that maybe i can use rtkdrawgeometricphantom
>>>> to generate a reference volume. However,
>>>> I noticed that in  the ADMMTV example in RTK wiki page,
>>>> <http://wiki.openrtk.org/index.php/RTK/Examples/ADMMTVReconstruction>
>>>> when i use the default demand, it works well (both for rtkadmmtotalvariation
>>>> and rtkdrawgeometricphantom)
>>>> . But when i change the spacing from 2 to 1, and dimension as 128.
>>>> i.e. the commands
>>>> from
>>>> rtkdrawgeometricphantom --spacing 2 --dimension 256--phantomfile
>>>> SheppLogan.txt -o ref.mha
>>>> to
>>>>
>>>> rtkdrawgeometricphantom --spacing 1 --dimension 128 --phantomfile SheppLogan.txt -o ref.mha
>>>>
>>>> the volume's visualization(ref.mha) is wired .
>>>>
>>>> So can you help me to find what's going on or tell me a better way to make the comparison between RTK method and my implementations.
>>>>
>>>>
>>>> Thanks in advance and with my best regards
>>>>
>>>> Guangming
>>>>
>>>>
>>>> *Guangming Zang (Alex)*
>>>> *King Abdullah University of Science and Technology(KAUST)*
>>>> *University of Chinese Academy of Sciences(UCAS)*
>>>>
>>>>
>>>>
>>>>
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>>
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