[Rtk-users] Reconstruction problems

[Arvid Piehl Lauritsen Böttiger]

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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