[Rtk-users] 4DROOSTERReconstruction example

Fri Oct 2 12:31:38 EDT 2015

Hi Simon and Cyril,

@Simon: I first run rtkfdk with some spacing/dimensions (ex: 0.88,512) and
then use itkSnap to create a mask from that 3D image. I then use that mask
as the input for ROOSTER, to which I again use the same spacing/dimensions.
For some values it seems to work and other it doesn't. I'm wondering if
itkSnap is truncating the spacing/dimension/origins when I save my mask,
and perhaps why something like (160,2,-159) works but (511,0.88,-224.84).
I'll take a look at the metadata.

I'll try resampling my masks and like you said that should probably fix my
issues.

Thanks for the help,
Joel

On Fri, Oct 2, 2015 at 12:53 AM, Cyril Mory <cyril.mory at uclouvain.be> wrote:

> Indeed, resampling the mask if needed, to the correct size, spacing,
> origin and direction, seems the simplest way to deal with this issue.
> But I would do it in the filter rather than in the application, so that
> anything built on top of ROOSTER (i.e. incremental ROOSTER, or the
> rtkfourdroostertest) also benefits from it.
> Feel free to do it if you want, otherwise I'll take care of it next week :)
>
>
> On 10/02/2015 08:44 AM, Simon Rit wrote:
>
> 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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