[Rtk-users] 4DROOSTERReconstruction example

[Joel Beaudry]

Hi Cyril,

The thing is I'm reconstructing a FDK image with dimensions 512 (0.88
spacing) and re-creating a mask off of that. So the motion mask should have
the same dimensions, spacing, and origin as the intended 4D image since I'm
using 4D rooster with --dimension 512 --spacing 0.88. Perhaps I'm creating
my mask incorrectly?

I'll try and fiddle with it a bit later and see why the mask I created for
160 (2), worked but not the case of 512 (0.88), and let you know what I
find.

Thanks again,
Joel

On Wed, Sep 30, 2015 at 12:33 AM, Cyril Mory <cyril.mory at uclouvain.be>
wrote:

> 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>
> 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 listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>>
>>
>
>
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