[Rtk-users] Reconstruction problems

[Cyril Mory]

Hi Arvid,

Unfortunately, you cannot do that. You have to obtain the exact geometry 
of this particular acquisition from the cone beam device you used.
If you need help to convert it to the RTK format, well, that's something 
you can ask for on this mailing list.
Can you get the geometry data ?

Regards,
Cyril

Le 12/10/2015 12:36, Arvid Piehl Lauritsen Böttiger a écrit :
> Sure.
>
> I'll admit I have yet to understand the specifics of the geometry
> file. Currently I just used a simulated one because that was what the
> SheppLogan example used, and the input projections looked similar.
>
> Here is a complete list of the commands I executed:
>
> rtksimulatedgeometry.exe -n 361 -o c:\Users\aplb\Work\out_dir\geometry360.xml
>
> rtkprojections.exe --path c:\Users\aplb\Work\tomography_data\dataset1\
> --output c:\Users\aplb\Work\out_dir\cylinder.mha --regexp .tif
>
> rtkfdk.exe -p c:\Users\aplb\Work\out_dir\ -r cylinder.mha -o
> c:\Users\aplb\Work\out_dir\cylinder_recon.mha -g
> c:\Users\aplb\Work\out_dir\geometry360.xml --spacing 2 --dimension 256
>
> I did not do anything to the contrast and that is most likely the
> issue. I downloaded and installed vv and I can see some (very unclear)
> features inside the SheppLogan reconstruction - so that's nice.
> However, currently I'm mostly interested in getting the geometry right :)
>
> best
>
> On Mon, Oct 12, 2015 at 11:54 AM, louie L <ghostcz at hotmail.com> wrote:
>> Hi,
>>
>> You can specify the size in each dimension. Can you post the arguments you used for the projections and reconstruction? Did you try to adjust the contrast of the output?
>>
>> Cheers,
>> Louie
>>
>> Sent from my iOS
>>
>>> On 12 Oct 2015, at 11:42, Arvid Piehl Lauritsen Böttiger <bottiger at gmail.com> wrote:
>>>
>>> Hi there
>>>
>>> I hope someone can help me me get started with RTK.
>>>
>>> First of all I should mention that I have compiled RTK on Windows 7
>>> using Visual Studio 2013. Everything seems to compile and run just
>>> fine.
>>>
>>> Secondly: I tried to reproduce this example:
>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK
>>>
>>> This was somewhat successful - I think. I could generate some
>>> projections, and reconstruct them. However, it just looks like an egg
>>> and not like a Shepp Logan phantom. See attachment.
>>>
>>> However, I'm unsure if this is expected or not. I took some homemade
>>> projections (of a small cylinder) and converted them into a MHA file
>>> (using rtkprojections.exe). The file looks correct in ImageJ. The
>>> dimensions are 370 pixels * 195 pixels * 361 projections
>>>
>>> You can get the file here:
>>> https://www.dropbox.com/s/p8tsgsh5xxb468f/cylinder.mha?dl=0
>>>
>>> The problem is that the reconstruction is wrong (see cylinder_recon).
>>> It looks like the dimensions are not read correctly, but I am unsure
>>> how I fix that? The rtkfdk.exe has a single --dimension parameter, but
>>> I am unsure which dimension that is suppose to be, but neither 195,
>>> 370 or any other value I could think of works for me.
>>>
>>> I hope someone can help me in the right direction.
>>>
>>> best
>>>
>>> Arvid
>>> <SheppLogan.PNG>
>>> <cylinder_recon.PNG>
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