[Rtk-users] 4DROOSTERReconstruction example

[Simon Rit]

Hi Joel,
Can you explain how you created your mask? Looking at the code, it seems to
me that if you create a 4D image with RTK, create a mask from this image
with exactly the same meta info and pass it to ROOSTER, that should work in
all cases. If I were you, I would compare the two mhd files (of the mask
and the 4D image you used to create it) and verify that the meta info is
exactly the same.
For ROOSTER, I suggest to add an interpolation when the information is not
inconsistent, e.g., in the main() function. I can do it if you agree Cyril.
Simon

On Thu, Oct 1, 2015 at 11:40 PM, Joel Beaudry <joelbeaudry at gmail.com> wrote:

> Hi Cyril,
>
> After trying out a few attempts, it seems like some values play nicer than
> others. Could it be an issue with floating point comparisons with the
> spacing and/or origins? It might explain why certain values seem to work
> (1.5) and others do not (0.88). I'll look at what values are being compared
> and get back to you.
>
> Thanks,
> Joel
>
> On Wed, Sep 30, 2015 at 12:51 PM, Joel Beaudry <joelbeaudry at gmail.com>
> wrote:
>
>> 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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