[Rtk-users] 4DROOSTERReconstruction example

[Cyril Mory]

Hi Joel,

Good to hear it's working now.
The error you get is explained on the wiki in the small paragraph after 
the cuda command line :

Note that the reconstructed volume in this example does not fully 
contain the attenuating object, causing hyper-attenuation artifacts on 
the borders of the result. To avoid these artifacts, reconstruct a 
larger volume (--dimension 256) should be fine. *Note that you will have 
to resize your motion mask as well, as 3D the motion mask is expected to 
have the same size, spacing and origin as the first 3 dimensions of the 
4D output. *

I guess I should take some time to fix that, and allow any motion mask, 
but until I do, you can resize your motion mask using the CLITK tools 
(http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you.

Cyril


On 09/29/2015 09:36 PM, Joel Beaudry wrote:
> Hi Cyril,
>
> Works like a charm, thanks! I tried it on some other datasets and it 
> seems to be working. I need to increase the resolution and play around 
> with the parameters now.
>
> I haven't had time to test it too much, but I do get an error when 
> attempting to reconstruct with different dimensions. I'm using Cuda, 
> and haven't tried it with just cpu reconstruction yet.
>
> i.e.)
> --dimension 160 --spacing 2 -> works
> --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In 
> AverageOutOfROIImageFilter: information of ROI image does not match 
> input image"
>
> I'll be able to test some other things later and list more details.
>
> Thanks,
> Joel
>
>
>
> On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory <cyril.mory at uclouvain.be 
> <mailto:cyril.mory at uclouvain.be>> wrote:
>
>     Hi Joel,
>
>     I have fixed the wiki example (command line parameters AND data).
>     Can you restart it from scratch and let me know if you still have
>     problems ?
>
>     Roughly, the problems were the following:
>     - the "mm_50.mha" motion mask file was not aligned with the CBCT
>     coordinates
>     - the regularization parameters (gamma space and gamma time) were
>     way too high. The regularization with a high gamma-time caused
>     frames to be identical, while it should only discourage variations
>
>     I hope it works, now. If it doesn't work for you, please keep asking
>     Cyril
>
>
>     On 09/28/2015 09:52 AM, Cyril Mory wrote:
>>     Hi Joel,
>>
>>     I have just tried to reproduce the wiki example, and indeed,
>>     there are several mistakes in it. I am working on correcting
>>     them. I'll keep you posted.
>>
>>     Cyril
>>
>>
>>     On 09/26/2015 05:32 AM, Joel Beaudry wrote:
>>>     Hi RTK-users,
>>>
>>>     I'm unable to reproduce the images from the
>>>     4DROOSTERReconstruction example. The 5 frames should show some
>>>     differences pertaining to patient motion but the ones that I'm
>>>     producing are identical, so no motion is visible.
>>>
>>>     Has anyone been able to follow the example and the provided
>>>     dataset to create a 4D image?
>>>
>>>     Thanks,
>>>     Joel
>>>
>>>
>>>     _______________________________________________
>>>     Rtk-users mailing list
>>>     Rtk-users at public.kitware.com  <mailto:Rtk-users at public.kitware.com>
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>>
>
>

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