<div dir="ltr"><div><div><div>Hi Joel,<br></div>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.<br></div>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.<br></div>Simon<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Oct 1, 2015 at 11:40 PM, Joel Beaudry <span dir="ltr"><<a href="mailto:joelbeaudry@gmail.com" target="_blank">joelbeaudry@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>Hi Cyril, <br><br></div>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.<br><br></div>Thanks, <br></div>Joel <br></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Sep 30, 2015 at 12:51 PM, Joel Beaudry <span dir="ltr"><<a href="mailto:joelbeaudry@gmail.com" target="_blank">joelbeaudry@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Hi Cyril, <br><br></div>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?<br><br></div>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.<br><br></div>Thanks again, <br></div>Joel<br></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Sep 30, 2015 at 12:33 AM, Cyril Mory <span dir="ltr"><<a href="mailto:cyril.mory@uclouvain.be" target="_blank">cyril.mory@uclouvain.be</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Joel,<br>
<br>
Good to hear it's working now.<br>
The error you get is explained on the wiki in the small paragraph
after the cuda command line :<br>
<br>
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. <b>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.
</b><br>
<br>
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 (<a href="http://www.creatis.insa-lyon.fr/rio/vv" target="_blank">http://www.creatis.insa-lyon.fr/rio/vv</a>) or any method
that suits you.<span><font color="#888888"><br>
<br>
Cyril</font></span><div><div><br>
<br>
<br>
<div>On 09/29/2015 09:36 PM, Joel Beaudry
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>Hi Cyril, <br>
<br>
</div>
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.<br>
<br>
</div>
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.<br>
<br>
</div>
i.e.) <br>
</div>
--dimension 160 --spacing 2 -> works<br>
</div>
--dimension 512,64,512 --spacing 0.88,2.5,0.88 -->
throws "In AverageOutOfROIImageFilter: information of ROI
image does not match input image"<br>
<br>
</div>
I'll be able to test some other things later and list more
details.<br>
<br>
</div>
Thanks, <br>
</div>
Joel<br>
<div>
<div>
<div><br>
<br>
</div>
</div>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Mon, Sep 28, 2015 at 4:48 AM, Cyril
Mory <span dir="ltr"><<a href="mailto:cyril.mory@uclouvain.be" target="_blank">cyril.mory@uclouvain.be</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi Joel,<br>
<br>
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 ? <br>
<br>
Roughly, the problems were the following: <br>
- the "mm_50.mha" motion mask file was not aligned with
the CBCT coordinates<br>
- 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<br>
<br>
I hope it works, now. If it doesn't work for you, please
keep asking<span><font color="#888888"><br>
Cyril</font></span>
<div>
<div><br>
<br>
<div>On 09/28/2015 09:52 AM, Cyril Mory wrote:<br>
</div>
<blockquote type="cite"> Hi Joel,<br>
<br>
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.<br>
<br>
Cyril<br>
<br>
<br>
<div>On 09/26/2015 05:32 AM, Joel Beaudry wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>
<div>
<div>Hi RTK-users, <br>
<br>
</div>
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. <br>
<br>
Has anyone been able to follow the example
and the provided dataset to create a 4D
image?<br>
<br>
</div>
Thanks, <br>
</div>
Joel<br>
</div>
<br>
<fieldset></fieldset>
<br>
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