<div dir="ltr"><div><div><div><div>Hi Simon and Cyril, <br><br></div>@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.<br><br></div>I'll try resampling my masks and like you said that should probably fix my issues.<br><br></div>Thanks for the help, <br></div>Joel<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Oct 2, 2015 at 12:53 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">
Indeed, resampling the mask if needed, to the correct size, spacing,
origin and direction, seems the simplest way to deal with this
issue.<br>
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. <br>
Feel free to do it if you want, otherwise I'll take care of it next
week :)<div><div class="h5"><br>
<br>
<div>On 10/02/2015 08:44 AM, Simon Rit
wrote:<br>
</div>
<blockquote type="cite">
<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>
<div>
<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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