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Hi Joel,<br>
<br>
I have just pushed a fix for this issue: in the 4DROOSTER filter, I
have added a resample filter between the ROI input and the
AverageOutOfROIImageFilter. On my side, it runs fine. Let me know if
it fixes the issue on your side.<br>
<br>
Thanks for pointing this out,<br>
Cyril<br>
<br>
<div class="moz-cite-prefix">On 10/02/2015 06:31 PM, Joel Beaudry
wrote:<br>
</div>
<blockquote
cite="mid:CAMyfbWrq0C5KSnSuaJf1Ld8kMb0etRsZJPbNB248jnL7Kk11eQ@mail.gmail.com"
type="cite">
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<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 moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true" 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>
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