'Re: [Insight-users] [ITK Community] Upsampling and Interpolators'

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List:       insight-users
Subject:    Re: [Insight-users] [ITK Community] Upsampling and Interpolators
From:       Bradley Lowekamp <blowekamp () mail ! nih ! gov>
Date:       2014-02-21 19:40:38
Message-ID: 7AA70F17-28BE-4EE9-A52B-BC7CC19AF431 () mail ! nih ! gov
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There is a separate filter which is optimized to just upscale an image by an integer \
factor, called "ExpandImageFilter". I have a little SimpleITK notebook on it here: \
http://simpleitk.github.io/SimpleITK-Notebooks/20_Expand_With_Interpolators.html

On Feb 21, 2014, at 2:36 PM, Dženan Zukić <dzenanz@gmail.com> wrote:

> You can upscale by a non-integer multiplier. In fact, you can change extent, \
> orientation of axes etc at the same time with a single resampling step. I don't \
> think that integer multiplier upscaling is optimized, so there should be no \
> performance penalty by not using that case. 
> 
> On Fri, Feb 21, 2014 at 3:33 PM, Jose Ignacio Prieto <joseignacio.prieto@gmail.com> \
> wrote: Thanks a lot Luis, 
> And does anybody know if you can upsample to a non integer multiplier of the \
> previous resolution. If so, does it have a performance penalty over an integer \
> multiplier? 
> Thanks
> 
> 
> On Wed, Feb 19, 2014 at 2:37 AM, Luis Ibanez <luis.ibanez@kitware.com> wrote:
> Hi Jose,
> 
> Yes, your intuition is correct in this case.
> 
> If you keep the images as a 4D image, the interpolator will
> indeed blend values across time points. Since after all, they
> are just seen as another spatial dimension.
> 
> 
> You may want to do the 3D resampling within the original
> 3D images, before you compose them into a 4D image.
> 
> 
> Note that since ITK 4.0 there is a set of classes in ITK
> for managing ND+Time.
> 
> 
> You will find them under
> 
> /ITK/Modules/Video/Core/include
> 
> 
> In particular,
> you may find interesting the class
> 
> itkVideoStream.h
> 
> 
> where you could put 3D images into a time sequence.
> 
> 
> Thanks
> 
> Luis
> 
> 
> 
> 
> On Tue, Feb 18, 2014 at 4:40 PM, Jose Ignacio Prieto <joseignacio.prieto@gmail.com> \
> wrote: Hi all, I am trying to upsample an image using this example as base \
> http://www.itk.org/Doxygen/html/Filtering_2ResampleVolumesToBeIsotropic_8cxx-example.html#_a5
>  I have MRI cine data with spacing like 1:1:8. I mounted all time frames into a 4D \
> image and I would like to upsample on Z axis to get 1:1:1. I was wondering if I \
> should better divide the 4D image  into a vector of 3D images so the interpolator \
> wouldn't mix different times frames or it doesn't matter. ( also because I am \
> interested in performance). Is it ok to use the linear interpolator for MRI? Or I \
> should use BSPline? If so, is it faster to work on 3D  for the splines??  
> Thank you very much
> 
> Ignacio Prieto
> 
> Software Developer
> Biomedical Imaging Center
> Pontificia Universidad Católica de Chile
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
> 
> _______________________________________________
> Community mailing list
> Community@itk.org
> http://public.kitware.com/cgi-bin/mailman/listinfo/community
> 
> 
> 
> 
> 
> -- 
> José Ignacio Prieto
> celular(nuevo): 94348182
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
> 
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
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[Attachment #5 (unknown)]

<html><head><meta http-equiv="Content-Type" content="text/html \
charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; \
-webkit-line-break: after-white-space;">There is a separate filter which is optimized \
to just upscale an image by an integer factor, called "ExpandImageFilter". I have a \
little SimpleITK notebook on it here:<div><a \
href="http://simpleitk.github.io/SimpleITK-Notebooks/20_Expand_With_Interpolators.html \
">http://simpleitk.github.io/SimpleITK-Notebooks/20_Expand_With_Interpolators.html</a></div><div><br></div><div><br><div><div>On \
Feb 21, 2014, at 2:36 PM, Dženan Zukić &lt;<a \
href="mailto:dzenanz@gmail.com">dzenanz@gmail.com</a>&gt; wrote:</div><br \
class="Apple-interchange-newline"><blockquote type="cite"><meta \
http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr"><div \
class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">You can \
upscale by a non-integer multiplier. In fact, you can change extent, orientation of \
axes etc at the same time with a single resampling step. I don't think that integer \
multiplier upscaling is optimized, so there should be no performance penalty by not \
using that case.</div>

</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Feb 21, 2014 \
at 3:33 PM, Jose Ignacio Prieto <span dir="ltr">&lt;<a \
href="mailto:joseignacio.prieto@gmail.com" \
target="_blank">joseignacio.prieto@gmail.com</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc \
solid;padding-left:1ex"><div dir="ltr">Thanks a lot Luis,&nbsp;<div>And does anybody \
know if you can upsample to a non integer multiplier of the previous resolution. If \
so, does it have a performance penalty over an integer multiplier?<div>

<br></div><div>
Thanks</div></div></div><div class="gmail_extra"><div><div class="h5"><br><br><div \
class="gmail_quote">On Wed, Feb 19, 2014 at 2:37 AM, Luis Ibanez <span \
dir="ltr">&lt;<a href="mailto:luis.ibanez@kitware.com" \
target="_blank">luis.ibanez@kitware.com</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc \
solid;padding-left:1ex"><div dir="ltr">Hi Jose,<div><br></div><div>Yes, your \
intuition is correct in this case.</div><div><br></div><div>If you keep the images as \
a 4D image, the interpolator will</div>

<div>indeed blend values across time points. Since after all, they</div>
<div>are just seen as another spatial \
dimension.</div><div><br></div><div><br></div><div>You may want to do the 3D \
resampling within the original</div><div>3D images, before you compose them into a 4D \
image.</div><div><br>

</div><div><br></div><div>Note that since ITK 4.0 there is a set of classes in \
ITK</div><div>for managing ND+Time.</div><div><br></div><div><br></div><div>You will \
find them under</div><div><br></div><div>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; \
&nbsp; &nbsp; /ITK/Modules/Video/Core/include<br>

</div><div><br></div><div><br></div><div>In particular,</div><div>you may find \
interesting the class</div><div><br></div><div>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; \
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; \
&nbsp;itkVideoStream.h<br></div><div><br></div><div><br></div><div>where you could \
put 3D images into a time sequence.</div>

<div><br></div><div><br></div><div>&nbsp; &nbsp; \
Thanks</div><div><br></div><div>&nbsp; &nbsp; &nbsp; &nbsp; \
&nbsp;Luis</div><div><br></div><div><br></div></div><div \
class="gmail_extra"><br><br><div class="gmail_quote"><div>On Tue, Feb 18, 2014 at \
4:40 PM, Jose Ignacio Prieto <span dir="ltr">&lt;<a \
href="mailto:joseignacio.prieto@gmail.com" \
target="_blank">joseignacio.prieto@gmail.com</a>&gt;</span> wrote:<br>

</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc \
solid;padding-left:1ex"><div><div dir="ltr">Hi all, I am trying to upsample an image \
using this example as base&nbsp;<a \
href="http://www.itk.org/Doxygen/html/Filtering_2ResampleVolumesToBeIsotropic_8cxx-example.html#_a5" \
target="_blank">http://www.itk.org/Doxygen/html/Filtering_2ResampleVolumesToBeIsotropic_8cxx-example.html#_a5</a><div>

I have MRI cine data with spacing like 1:1:8. I mounted all time frames into a 4D \
image and I would like to upsample on Z axis to get 1:1:1. I was wondering if I \
should better divide the 4D image &nbsp;into a vector of 3D images so the \
interpolator wouldn't mix different times frames or it doesn't matter. ( also because \
I am interested in performance). Is it ok to use the linear interpolator for MRI? Or \
I should use BSPline? If so, is it faster to work on 3D &nbsp;for the \
splines??&nbsp;</div>

<div><br></div><div>Thank you very much</div><div><br></div><div>Ignacio \
Prieto</div><div><br></div><div>Software Developer</div><div>Biomedical Imaging \
Center</div><div>Pontificia Universidad Católica de Chile</div></div>

<br></div>_____________________________________<br>
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<br></blockquote></div><br></div> </blockquote></div><br><br \
clear="all"><div><br></div></div></div><span class="HOEnZb"><font color="#888888">-- \
<br>José Ignacio Prieto<br>celular(nuevo): 94348182 </font></span></div>
<br>_____________________________________<br>
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<br></blockquote></div><br></div> _____________________________________<br>Powered by \
<a href="http://www.kitware.com">www.kitware.com</a><br><br>Visit other Kitware \
open-source projects at<br><a \
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offers ITK Training Courses, for more information \
visit:<br>http://www.kitware.com/products/protraining.php<br><br>Please keep messages \
on-topic and check the ITK FAQ at:<br>http://www.itk.org/Wiki/ITK_FAQ<br><br>Follow \
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